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HEADER OXYGEN STORAGE/TRANSPORT 08-AUG-06 2HZ1 TITLE THE X-RAY CRYSTAL STRUCTURE OF FERROUS SYNECHOCYSTIS TITLE 2 HEMOGLOBIN WITH A COVALENT LINKAGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYANOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HEMOGLOBIN, HB; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP.; SOURCE 3 STRAIN: PCC 6803; SOURCE 4 GENE: GLBN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA KEYWDS SYNECHOCYSTIS, HEMOGLOBIN, HEME, GLOBIN, FERROUS, KEYWDS 2 HEXACOORDINATE, COVALENT HEME VINYL LINK EXPDTA X-RAY DIFFRACTION AUTHOR J.A.HOY REVDAT 2 13-FEB-07 2HZ1 1 JRNL REVDAT 1 29-AUG-06 2HZ1 0 JRNL AUTH J.A.HOY,B.J.SMAGGHE,P.HALDER,M.S.HARGROVE JRNL TITL COVALENT HEME ATTACHMENT IN SYNECHOCYSTIS JRNL TITL 2 HEMOGLOBIN IS REQUIRED TO PREVENT FERROUS HEME JRNL TITL 3 DISSOCIATION JRNL REF PROTEIN SCI. V. 16 250 2007 JRNL REFN ASTM PRCIEI US ISSN 0961-8368 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 11435 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 598 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 823 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS : 1154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.09000 REMARK 3 B22 (A**2) : -0.73000 REMARK 3 B33 (A**2) : 0.83000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.142 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.856 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1044 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 908 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1417 ; 1.596 ; 2.011 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2100 ; 0.958 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 122 ; 5.345 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 146 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1192 ; 0.016 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 221 ; 0.016 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 308 ; 0.256 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1095 ; 0.238 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 529 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 90 ; 0.267 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.011 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 19 ; 0.331 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 45 ; 0.285 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.226 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 608 ; 0.946 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 962 ; 1.723 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 436 ; 2.710 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 455 ; 4.181 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 0 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 0 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 2HZ1 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 3.101 (2007-05-29) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB . REMARK 100 THE RCSB ID CODE IS RCSB038930. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-2005 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11435 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 37.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.830 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : 0.24800 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.68 REMARK 200 R MERGE FOR SHELL (I) : 0.14300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1RTX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 31% PEG MME 5000, 0.1 M MES, 0.2 M REMARK 280 AMMONIUM SULFATE, 0.01 M CADMIUM CHLORIDE, 0.01 M SODIUM REMARK 280 HEPES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+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 21.33100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.31050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.25150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.31050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.33100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.25150 REMARK 290 SMTRY3 4 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 1 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 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 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O HOH 113 O HOH 128 1.39 REMARK 500 OG1 THR A 3 O HOH 18 1.74 REMARK 500 O1 SO3 204 O HOH 7 1.98 REMARK 500 NZ LYS A 71 O HOH 64 2.08 REMARK 500 N SER A 2 O HOH 29 2.17 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 66 SD MET A 66 CE -0.127 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 79 DISTANCE = 5.47 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HZ2 RELATED DB: PDB REMARK 900 RELATED ID: 2HZ3 RELATED DB: PDB REMARK 900 RELATED ID: 1RTX RELATED DB: PDB DBREF 2HZ1 A 2 124 UNP P73925 GLBN_SYNY3 2 124 SEQRES 1 A 123 SER THR LEU TYR GLU LYS LEU GLY GLY THR THR ALA VAL SEQRES 2 A 123 ASP LEU ALA VAL ASP LYS PHE TYR GLU ARG VAL LEU GLN SEQRES 3 A 123 ASP ASP ARG ILE LYS HIS PHE PHE ALA ASP VAL ASP MET SEQRES 4 A 123 ALA LYS GLN ARG ALA HIS GLN LYS ALA PHE LEU THR TYR SEQRES 5 A 123 ALA PHE GLY GLY THR ASP LYS TYR ASP GLY ARG TYR MET SEQRES 6 A 123 ARG GLU ALA HIS LYS GLU LEU VAL GLU ASN HIS GLY LEU SEQRES 7 A 123 ASN GLY GLU HIS PHE ASP ALA VAL ALA GLU ASP LEU LEU SEQRES 8 A 123 ALA THR LEU LYS GLU MET GLY VAL PRO GLU ASP LEU ILE SEQRES 9 A 123 ALA GLU VAL ALA ALA VAL ALA GLY ALA PRO ALA HIS LYS SEQRES 10 A 123 ARG ASP VAL LEU ASN GLN HET CD 201 1 HET CD 202 1 HET SO3 204 4 HET HEM A 125 43 HET SO2 203 3 HET SO2 205 3 HETNAM CD CADMIUM ION HETNAM SO3 SULFITE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM SO2 SULFUR DIOXIDE HETSYN HEM HEME FORMUL 2 CD 2(CD 2+) FORMUL 4 SO3 O3 S 2- FORMUL 5 HEM C34 H32 FE N4 O4 FORMUL 6 SO2 2(O2 S) FORMUL 8 HOH *130(H2 O) HELIX 1 1 THR A 3 GLY A 9 1 7 HELIX 2 2 GLY A 10 GLN A 27 1 18 HELIX 3 3 ILE A 31 ALA A 36 5 6 HELIX 4 4 ASP A 39 GLY A 56 1 18 HELIX 5 5 GLY A 57 TYR A 61 5 5 HELIX 6 6 ASP A 62 HIS A 77 1 16 HELIX 7 7 ASN A 80 MET A 98 1 19 HELIX 8 8 PRO A 101 GLY A 113 1 13 HELIX 9 9 ALA A 114 LEU A 122 1 9 LINK NE2 HIS A 46 FE HEM A 125 LINK NE2 HIS A 70 FE HEM A 125 CRYST1 42.662 46.503 62.621 90.00 90.00 90.00 P 21 21 21 4 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 0.023440 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021504 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015969 0.00000