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HEADER OXYGEN STORAGE/TRANSPORT 05-APR-01 1IDR TITLE CRYSTAL STRUCTURE OF THE TRUNCATED-HEMOGLOBIN-N FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN HBN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_COMMON: BACTERIA; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA KEYWDS TRUNCATED HEMOGLOBIN FOLD EXPDTA X-RAY DIFFRACTION AUTHOR M.MILANI,A.PESCE,P.ASCENZI,M.GUERTIN,M.BOLOGNESI REVDAT 1 22-AUG-01 1IDR 0 JRNL AUTH M.MILANI,A.PESCE,Y.OUELLET,P.ASCENZI,M.GUERTIN, JRNL AUTH 2 M.BOLOGNESI JRNL TITL MYCOBACTERIUM TUBERCULOSIS HEMOGLOBIN N DISPLAYS A JRNL TITL 2 PROTEIN TUNNEL SUITED FOR O2 DIFFUSION TO THE HEME. JRNL REF EMBO J. V. 20 3902 2001 JRNL REFN ASTM EMJODG UK ISSN 0261-4189 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 18688 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1910 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 105 REMARK 3 SOLVENT ATOMS : 228 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.35000 REMARK 3 B22 (A**2) : 0.72000 REMARK 3 B33 (A**2) : -1.07000 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): 0.176 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.169 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.432 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.012 ; 0.021 REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 7.962 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 8.767 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 13.994; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 13.303; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IDR 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 (2007-03-17) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB . REMARK 100 THE RCSB ID CODE IS RCSB013186. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-2000 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.30 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18688 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 10.200 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM PHOSPHATE, PH 8.3, REMARK 280 MICRODIALYSIS, TEMPERATURE 277K 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 22.40000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.51000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.12400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.51000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.12400 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 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 300 GEL-FILTRATION EXPERIMENT INDICATES THAT THE PROTEIN REMARK 300 IS LOOSELY DIMERIC. 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 129 REMARK 465 GLU A 130 REMARK 465 SER A 131 REMARK 465 THR A 132 REMARK 465 THR A 133 REMARK 465 ALA A 134 REMARK 465 PRO A 135 REMARK 465 VAL A 136 REMARK 465 MET B 1 REMARK 465 SER B 128 REMARK 465 GLY B 129 REMARK 465 GLU B 130 REMARK 465 SER B 131 REMARK 465 THR B 132 REMARK 465 THR B 133 REMARK 465 ALA B 134 REMARK 465 PRO B 135 REMARK 465 VAL B 136 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 128 O REMARK 470 THR B 127 O 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 22 O HOH 51 2.14 REMARK 500 O HOH 150 O HOH 158 2.16 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH 81 O HOH 223 1565 1.98 DBREF 1IDR A 1 136 UNP P0A592 GLBN_MYCTU 1 136 DBREF 1IDR B 1 136 UNP P0A592 GLBN_MYCTU 1 136 SEQRES 1 A 136 MET GLY LEU LEU SER ARG LEU ARG LYS ARG GLU PRO ILE SEQRES 2 A 136 SER ILE TYR ASP LYS ILE GLY GLY HIS GLU ALA ILE GLU SEQRES 3 A 136 VAL VAL VAL GLU ASP PHE TYR VAL ARG VAL LEU ALA ASP SEQRES 4 A 136 ASP GLN LEU SER ALA PHE PHE SER GLY THR ASN MET SER SEQRES 5 A 136 ARG LEU LYS GLY LYS GLN VAL GLU PHE PHE ALA ALA ALA SEQRES 6 A 136 LEU GLY GLY PRO GLU PRO TYR THR GLY ALA PRO MET LYS SEQRES 7 A 136 GLN VAL HIS GLN GLY ARG GLY ILE THR MET HIS HIS PHE SEQRES 8 A 136 SER LEU VAL ALA GLY HIS LEU ALA ASP ALA LEU THR ALA SEQRES 9 A 136 ALA GLY VAL PRO SER GLU THR ILE THR GLU ILE LEU GLY SEQRES 10 A 136 VAL ILE ALA PRO LEU ALA VAL ASP VAL THR SER GLY GLU SEQRES 11 A 136 SER THR THR ALA PRO VAL SEQRES 1 B 136 MET GLY LEU LEU SER ARG LEU ARG LYS ARG GLU PRO ILE SEQRES 2 B 136 SER ILE TYR ASP LYS ILE GLY GLY HIS GLU ALA ILE GLU SEQRES 3 B 136 VAL VAL VAL GLU ASP PHE TYR VAL ARG VAL LEU ALA ASP SEQRES 4 B 136 ASP GLN LEU SER ALA PHE PHE SER GLY THR ASN MET SER SEQRES 5 B 136 ARG LEU LYS GLY LYS GLN VAL GLU PHE PHE ALA ALA ALA SEQRES 6 B 136 LEU GLY GLY PRO GLU PRO TYR THR GLY ALA PRO MET LYS SEQRES 7 B 136 GLN VAL HIS GLN GLY ARG GLY ILE THR MET HIS HIS PHE SEQRES 8 B 136 SER LEU VAL ALA GLY HIS LEU ALA ASP ALA LEU THR ALA SEQRES 9 B 136 ALA GLY VAL PRO SER GLU THR ILE THR GLU ILE LEU GLY SEQRES 10 B 136 VAL ILE ALA PRO LEU ALA VAL ASP VAL THR SER GLY GLU SEQRES 11 B 136 SER THR THR ALA PRO VAL HET PO4 301 5 HET PO4 302 5 HET PO4 303 5 HET HEM A 144 43 HET HEM B 144 43 HET OXY A 145 2 HET OXY B 145 2 HETNAM PO4 PHOSPHATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM OXY OXYGEN MOLECULE HETSYN HEM HEME FORMUL 3 PO4 3(O4 P 3-) FORMUL 6 HEM 2(C34 H32 FE N4 O4) FORMUL 8 OXY 2(O2) FORMUL 10 HOH *228(H2 O) HELIX 1 1 GLY A 2 LYS A 9 1 8 HELIX 2 2 SER A 14 ILE A 19 1 6 HELIX 3 3 GLY A 20 ASP A 39 1 20 HELIX 4 4 LEU A 42 SER A 47 5 6 HELIX 5 5 ASN A 50 LEU A 66 1 17 HELIX 6 6 PRO A 76 GLN A 82 1 7 HELIX 7 7 THR A 87 ALA A 105 1 19 HELIX 8 8 PRO A 108 ALA A 120 1 13 HELIX 9 9 LEU A 122 THR A 127 1 6 HELIX 10 10 GLY B 2 LYS B 9 1 8 HELIX 11 11 SER B 14 ILE B 19 1 6 HELIX 12 12 GLY B 20 ALA B 38 1 19 HELIX 13 13 LEU B 42 SER B 47 5 6 HELIX 14 14 ASN B 50 LEU B 66 1 17 HELIX 15 15 PRO B 76 GLN B 82 1 7 HELIX 16 16 THR B 87 ALA B 105 1 19 HELIX 17 17 PRO B 108 ALA B 120 1 13 HELIX 18 18 LEU B 122 THR B 127 1 6 LINK FE HEM A 144 NE2 HIS A 81 LINK FE HEM A 144 O1 OXY A 145 LINK FE HEM B 144 NE2 HIS B 81 LINK FE HEM B 144 O1 OXY B 145 CRYST1 44.800 62.248 91.020 90.00 90.00 90.00 P 21 21 21 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 0.022321 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016065 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010987 0.00000