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HEADER OXYGEN TRANSPORT 19-FEB-97 1VHB TITLE BACTERIAL DIMERIC HEMOGLOBIN FROM VITREOSCILLA STERCORARIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SOLUBLE CYTOCHROME O; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VITREOSCILLA STERCORARIA; SOURCE 3 STRAIN: C1; SOURCE 4 ATCC: 15218; SOURCE 5 GENE: VGB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5-ALPHA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACTERIAL; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDH88; SOURCE 10 EXPRESSION_SYSTEM_GENE: VGB KEYWDS HEME, RESPIRATORY PROTEIN, OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.TARRICONE,A.GALIZZI,A.CODA,P.ASCENZI,M.BOLOGNESI REVDAT 1 25-FEB-98 1VHB 0 JRNL AUTH C.TARRICONE,A.GALIZZI,A.CODA,P.ASCENZI,M.BOLOGNESI JRNL TITL UNUSUAL STRUCTURE OF THE OXYGEN-BINDING SITE IN JRNL TITL 2 THE DIMERIC BACTERIAL HEMOGLOBIN FROM VITREOSCILLA JRNL TITL 3 SP. JRNL REF STRUCTURE V. 5 497 1997 JRNL REFN ASTM STRUE6 UK ISSN 0969-2126 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT V. 1 REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 27040 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD :A POSTERIORI REMARK 3 FREE R VALUE TEST SET SELECTION :EVERY 24TH REFLECTION REMARK 3 R VALUE (WORKING + TEST SET) :NULL REMARK 3 R VALUE (WORKING SET) :0.184 REMARK 3 FREE R VALUE :0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) :4.100 REMARK 3 FREE R VALUE TEST SET COUNT :1100 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1840 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 4.10 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1100 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 27040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2042 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 35.000 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.011 ; 24.000; 2178 REMARK 3 BOND ANGLES (DEGREES) : 1.788 ; 13.000; 2956 REMARK 3 TORSION ANGLES (DEGREES) : 13.148; 15.000; 1236 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.015 ; 20.000; 54 REMARK 3 GENERAL PLANES (A) : 0.017 ; 50.000; 302 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 4.478 ; 10.000; 2078 REMARK 3 NON-BONDED CONTACTS (A) : 0.043 ; 100.000; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.58 REMARK 3 BSOL : 167.00 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VHB 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 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-1996 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 6.40 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : DW21B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, ROTAVATA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26582 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : 0.36000 REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : 0.36000 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIR-DENSITY MODIFICATION REMARK 200 SOFTWARE USED: SCALEIT, SHELX-90, MLPHARE, SOLOMON, DM, GLRF, REMARK 200 NCSMASK REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PRECIPITANT: AMMONIUM SULFATE 1.2 REMARK 280 M. BUFFER: PYROPHOSPHATE 0.2 M PH 6.4. ADDITIVES: ETHYLENE REMARK 280 GLYCOL 3% V/V. PROTEIN CONCENTRATION 25 MG/ML. VAPOR DIFFUSION REMARK 280 TECHNIQUES., VAPOR DIFFUSION 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 20.71000 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 2 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 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 ASP A 44 REMARK 465 MET A 45 REMARK 465 GLY A 46 REMARK 465 ARG A 47 REMARK 465 GLN A 48 REMARK 465 GLU A 49 REMARK 465 SER A 50 REMARK 465 LEU A 51 REMARK 465 GLU A 52 REMARK 465 GLU A 146 REMARK 465 MET B 1 REMARK 465 ASP B 44 REMARK 465 MET B 45 REMARK 465 GLY B 46 REMARK 465 ARG B 47 REMARK 465 GLN B 48 REMARK 465 GLU B 49 REMARK 465 SER B 50 REMARK 465 LEU B 51 REMARK 465 GLU B 52 REMARK 465 GLU B 146 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU B 110 CA - CB - CG ANGL. DEV. =-12.8 DEGREES DBREF 1VHB A 1 146 UNP P04252 BAHG_VITST 1 146 DBREF 1VHB B 1 146 UNP P04252 BAHG_VITST 1 146 SEQRES 1 A 146 MET LEU ASP GLN GLN THR ILE ASN ILE ILE LYS ALA THR SEQRES 2 A 146 VAL PRO VAL LEU LYS GLU HIS GLY VAL THR ILE THR THR SEQRES 3 A 146 THR PHE TYR LYS ASN LEU PHE ALA LYS HIS PRO GLU VAL SEQRES 4 A 146 ARG PRO LEU PHE ASP MET GLY ARG GLN GLU SER LEU GLU SEQRES 5 A 146 GLN PRO LYS ALA LEU ALA MET THR VAL LEU ALA ALA ALA SEQRES 6 A 146 GLN ASN ILE GLU ASN LEU PRO ALA ILE LEU PRO ALA VAL SEQRES 7 A 146 LYS LYS ILE ALA VAL LYS HIS CYS GLN ALA GLY VAL ALA SEQRES 8 A 146 ALA ALA HIS TYR PRO ILE VAL GLY GLN GLU LEU LEU GLY SEQRES 9 A 146 ALA ILE LYS GLU VAL LEU GLY ASP ALA ALA THR ASP ASP SEQRES 10 A 146 ILE LEU ASP ALA TRP GLY LYS ALA TYR GLY VAL ILE ALA SEQRES 11 A 146 ASP VAL PHE ILE GLN VAL GLU ALA ASP LEU TYR ALA GLN SEQRES 12 A 146 ALA VAL GLU SEQRES 1 B 146 MET LEU ASP GLN GLN THR ILE ASN ILE ILE LYS ALA THR SEQRES 2 B 146 VAL PRO VAL LEU LYS GLU HIS GLY VAL THR ILE THR THR SEQRES 3 B 146 THR PHE TYR LYS ASN LEU PHE ALA LYS HIS PRO GLU VAL SEQRES 4 B 146 ARG PRO LEU PHE ASP MET GLY ARG GLN GLU SER LEU GLU SEQRES 5 B 146 GLN PRO LYS ALA LEU ALA MET THR VAL LEU ALA ALA ALA SEQRES 6 B 146 GLN ASN ILE GLU ASN LEU PRO ALA ILE LEU PRO ALA VAL SEQRES 7 B 146 LYS LYS ILE ALA VAL LYS HIS CYS GLN ALA GLY VAL ALA SEQRES 8 B 146 ALA ALA HIS TYR PRO ILE VAL GLY GLN GLU LEU LEU GLY SEQRES 9 B 146 ALA ILE LYS GLU VAL LEU GLY ASP ALA ALA THR ASP ASP SEQRES 10 B 146 ILE LEU ASP ALA TRP GLY LYS ALA TYR GLY VAL ILE ALA SEQRES 11 B 146 ASP VAL PHE ILE GLN VAL GLU ALA ASP LEU TYR ALA GLN SEQRES 12 B 146 ALA VAL GLU HET HEM A 150 43 HET HEM B 150 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 HOH *119(H2 O) HELIX 1 1 GLN A 4 LYS A 35 1 32 HELIX 2 2 PRO A 37 LEU A 42 1 6 HELIX 3 3 LEU A 57 ALA A 88 1 32 HELIX 4 4 ALA A 92 ALA A 113 1 22 HELIX 5 5 ASP A 116 ALA A 144 1 29 HELIX 6 6 GLN B 4 LYS B 35 1 32 HELIX 7 7 PRO B 37 LEU B 42 5 6 HELIX 8 8 LEU B 57 GLN B 66 1 10 HELIX 9 9 ILE B 68 ALA B 88 5 21 HELIX 10 10 ALA B 92 ALA B 113 1 22 HELIX 11 11 ASP B 116 GLN B 143 1 28 LINK FE HEM A 150 NE2 HIS A 85 LINK FE HEM B 150 NE2 HIS B 85 CRYST1 63.320 41.420 62.940 90.00 106.17 90.00 P 1 21 1 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 0.015793 0.000000 0.004579 0.00000 SCALE2 0.000000 0.024143 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016543 0.00000 MTRIX1 1 0.268080 0.000000 -0.963400 68.79999 1 MTRIX2 1 0.000000 -1.000000 0.000000 20.77000 1 MTRIX3 1 -0.963400 0.000000 -0.268080 90.56000 1