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HEADER OXYGEN TRANSPORT 11-JUN-98 1CH4 TITLE MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA (F133V) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS OXYGEN TRANSPORT, CHIMERA PROTEIN, RESPIRATORY PROTEIN, HEME EXPDTA X-RAY DIFFRACTION AUTHOR T.SHIRAI,M.FUJIKAKE,T.YAMANE,K.INABA,K.ISHIMORI,I.MORISHIMA REVDAT 1 27-APR-99 1CH4 0 JRNL AUTH T.SHIRAI,M.FUJIKAKE,T.YAMANE,K.INABA,K.ISHIMORI, JRNL AUTH 2 I.MORISHIMA JRNL TITL CRYSTAL STRUCTURE OF A PROTEIN WITH AN ARTIFICIAL JRNL TITL 2 EXON-SHUFFLING, MODULE M4-SUBSTITUTED CHIMERA JRNL TITL 3 HEMOGLOBIN BETA ALPHA, AT 2.5 A RESOLUTION. JRNL REF J.MOL.BIOL. V. 287 369 1999 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.SHIRAI,M.FUJIKAKE,T.YAMANE,K.INABA,K.ISHIMORI, REMARK 1 AUTH 2 I.MORISHIMA REMARK 1 TITL DESIGN, CONSTRUCTION, CRYSTALLIZATION, AND REMARK 1 TITL 2 PRELIMINARY X-RAY STUDIES OF A FINE-TUNING MUTANT REMARK 1 TITL 3 (F133V) OF MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN REMARK 1 REF PROTEINS: STRUCT.,FUNCT., V. 32 263 1998 REMARK 1 REF 2 GENET. REMARK 1 REFN ASTM PSFGEY US ISSN 0887-3585 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 81.4 REMARK 3 NUMBER OF REFLECTIONS : 15212 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDAM REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 787 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4528 REMARK 3 NUCLEIC ACID ATOMS : NULL REMARK 3 HETEROGEN ATOMS : 180 REMARK 3 SOLVENT ATOMS : 42 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 7.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 2.65 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.48 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : STRICT REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : PARAM19X.HEME REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19X.HEME REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CH4 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-16) REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : OCT-1996 REMARK 200 TEMPERATURE (KELVIN) : 291.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU/MSC RU-H3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17766 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: CN-HEMOGLOBIN H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,1/2+Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 40.65500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 SEQRES 1 A 146 VAL HIS LEU THR PRO GLU GLU LYS SER ALA VAL THR ALA SEQRES 2 A 146 LEU TRP GLY LYS VAL ASN VAL ASP GLU VAL GLY GLY GLU SEQRES 3 A 146 ALA LEU GLY ARG LEU LEU VAL VAL TYR PRO TRP THR GLN SEQRES 4 A 146 ARG PHE PHE GLU SER PHE GLY ASP LEU SER THR PRO ASP SEQRES 5 A 146 ALA VAL MET GLY ASN PRO LYS VAL LYS ALA HIS GLY LYS SEQRES 6 A 146 LYS VAL LEU GLY ALA PHE SER ASP GLY LEU ALA HIS LEU SEQRES 7 A 146 ASP ASN LEU LYS GLY THR PHE ALA THR LEU SER GLU LEU SEQRES 8 A 146 HIS CYS ASP LYS LEU ARG VAL ASP PRO VAL ASN PHE LYS SEQRES 9 A 146 LEU LEU SER HIS CYS LEU LEU VAL THR LEU ALA ALA HIS SEQRES 10 A 146 LEU PRO ALA GLU PHE THR PRO ALA VAL HIS ALA SER LEU SEQRES 11 A 146 ASP LYS VAL LEU ALA SER VAL SER THR VAL LEU THR SER SEQRES 12 A 146 LYS TYR ARG SEQRES 1 B 146 VAL HIS LEU THR PRO GLU GLU LYS SER ALA VAL THR ALA SEQRES 2 B 146 LEU TRP GLY LYS VAL ASN VAL ASP GLU VAL GLY GLY GLU SEQRES 3 B 146 ALA LEU GLY ARG LEU LEU VAL VAL TYR PRO TRP THR GLN SEQRES 4 B 146 ARG PHE PHE GLU SER PHE GLY ASP LEU SER THR PRO ASP SEQRES 5 B 146 ALA VAL MET GLY ASN PRO LYS VAL LYS ALA HIS GLY LYS SEQRES 6 B 146 LYS VAL LEU GLY ALA PHE SER ASP GLY LEU ALA HIS LEU SEQRES 7 B 146 ASP ASN LEU LYS GLY THR PHE ALA THR LEU SER GLU LEU SEQRES 8 B 146 HIS CYS ASP LYS LEU ARG VAL ASP PRO VAL ASN PHE LYS SEQRES 9 B 146 LEU LEU SER HIS CYS LEU LEU VAL THR LEU ALA ALA HIS SEQRES 10 B 146 LEU PRO ALA GLU PHE THR PRO ALA VAL HIS ALA SER LEU SEQRES 11 B 146 ASP LYS VAL LEU ALA SER VAL SER THR VAL LEU THR SER SEQRES 12 B 146 LYS TYR ARG SEQRES 1 C 146 VAL HIS LEU THR PRO GLU GLU LYS SER ALA VAL THR ALA SEQRES 2 C 146 LEU TRP GLY LYS VAL ASN VAL ASP GLU VAL GLY GLY GLU SEQRES 3 C 146 ALA LEU GLY ARG LEU LEU VAL VAL TYR PRO TRP THR GLN SEQRES 4 C 146 ARG PHE PHE GLU SER PHE GLY ASP LEU SER THR PRO ASP SEQRES 5 C 146 ALA VAL MET GLY ASN PRO LYS VAL LYS ALA HIS GLY LYS SEQRES 6 C 146 LYS VAL LEU GLY ALA PHE SER ASP GLY LEU ALA HIS LEU SEQRES 7 C 146 ASP ASN LEU LYS GLY THR PHE ALA THR LEU SER GLU LEU SEQRES 8 C 146 HIS CYS ASP LYS LEU ARG VAL ASP PRO VAL ASN PHE LYS SEQRES 9 C 146 LEU LEU SER HIS CYS LEU LEU VAL THR LEU ALA ALA HIS SEQRES 10 C 146 LEU PRO ALA GLU PHE THR PRO ALA VAL HIS ALA SER LEU SEQRES 11 C 146 ASP LYS VAL LEU ALA SER VAL SER THR VAL LEU THR SER SEQRES 12 C 146 LYS TYR ARG SEQRES 1 D 146 VAL HIS LEU THR PRO GLU GLU LYS SER ALA VAL THR ALA SEQRES 2 D 146 LEU TRP GLY LYS VAL ASN VAL ASP GLU VAL GLY GLY GLU SEQRES 3 D 146 ALA LEU GLY ARG LEU LEU VAL VAL TYR PRO TRP THR GLN SEQRES 4 D 146 ARG PHE PHE GLU SER PHE GLY ASP LEU SER THR PRO ASP SEQRES 5 D 146 ALA VAL MET GLY ASN PRO LYS VAL LYS ALA HIS GLY LYS SEQRES 6 D 146 LYS VAL LEU GLY ALA PHE SER ASP GLY LEU ALA HIS LEU SEQRES 7 D 146 ASP ASN LEU LYS GLY THR PHE ALA THR LEU SER GLU LEU SEQRES 8 D 146 HIS CYS ASP LYS LEU ARG VAL ASP PRO VAL ASN PHE LYS SEQRES 9 D 146 LEU LEU SER HIS CYS LEU LEU VAL THR LEU ALA ALA HIS SEQRES 10 D 146 LEU PRO ALA GLU PHE THR PRO ALA VAL HIS ALA SER LEU SEQRES 11 D 146 ASP LYS VAL LEU ALA SER VAL SER THR VAL LEU THR SER SEQRES 12 D 146 LYS TYR ARG HET HEM A 147 43 HET CMO A 147 2 HET HEM B 147 43 HET CMO B 147 2 HET HEM C 147 43 HET CMO C 147 2 HET HEM D 147 43 HET CMO D 147 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CMO CARBON MONOXIDE HETSYN HEM HEME FORMUL 5 HEM 4(C34 H32 FE N4 O4) FORMUL 6 CMO 4(C O) FORMUL 13 HOH *42(H2 O) HELIX 1 1 PRO A 5 LYS A 17 1 13 HELIX 2 2 VAL A 20 VAL A 34 1 15 HELIX 3 3 PRO A 36 PHE A 45 5 10 HELIX 4 4 PRO A 51 GLY A 56 1 6 HELIX 5 5 PRO A 58 LEU A 75 1 18 HELIX 6 6 LEU A 81 ALA A 86 1 6 HELIX 7 7 THR A 87 ASP A 94 1 8 HELIX 8 8 PRO A 100 HIS A 117 1 18 HELIX 9 9 PRO A 124 THR A 142 1 19 HELIX 10 10 PRO B 5 LYS B 17 1 13 HELIX 11 11 VAL B 20 VAL B 34 1 15 HELIX 12 12 PRO B 36 PHE B 45 5 10 HELIX 13 13 PRO B 51 GLY B 56 1 6 HELIX 14 14 PRO B 58 LEU B 75 1 18 HELIX 15 15 LEU B 81 ALA B 86 1 6 HELIX 16 16 THR B 87 ASP B 94 1 8 HELIX 17 17 PRO B 100 HIS B 117 1 18 HELIX 18 18 PRO B 124 THR B 142 1 19 HELIX 19 19 PRO C 5 LYS C 17 1 13 HELIX 20 20 VAL C 20 VAL C 34 1 15 HELIX 21 21 PRO C 36 PHE C 45 5 10 HELIX 22 22 PRO C 51 GLY C 56 1 6 HELIX 23 23 PRO C 58 LEU C 75 1 18 HELIX 24 24 LEU C 81 PHE C 85 1 5 HELIX 25 25 THR C 87 CYS C 93 1 7 HELIX 26 26 PRO C 100 HIS C 117 1 18 HELIX 27 27 PRO C 124 LEU C 141 1 18 HELIX 28 28 PRO D 5 LYS D 17 1 13 HELIX 29 29 VAL D 20 VAL D 34 1 15 HELIX 30 30 PRO D 36 PHE D 45 5 10 HELIX 31 31 PRO D 51 GLY D 56 1 6 HELIX 32 32 PRO D 58 LEU D 75 1 18 HELIX 33 33 LEU D 81 PHE D 85 1 5 HELIX 34 34 THR D 87 CYS D 93 1 7 HELIX 35 35 PRO D 100 HIS D 117 1 18 HELIX 36 36 PRO D 124 LEU D 141 1 18 LINK FE HEM A 147 NE2 HIS A 92 LINK FE HEM A 147 C CMO A 147 LINK FE HEM B 147 NE2 HIS B 92 LINK FE HEM B 147 C CMO B 147 LINK FE HEM C 147 NE2 HIS C 92 LINK FE HEM C 147 C CMO C 147 LINK FE HEM D 147 NE2 HIS D 92 LINK FE HEM D 147 C CMO D 147 CRYST1 62.870 81.310 55.110 90.00 90.96 90.00 P 1 21 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015906 0.000000 0.000267 0.00000 SCALE2 0.000000 0.012299 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018148 0.00000 MTRIX1 1 -0.908143 -0.144029 -0.393105 36.64821 1 MTRIX2 1 -0.137863 -0.783712 0.605631 -4.80501 1 MTRIX3 1 -0.395310 0.604194 0.691867 10.26913 1