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HEADER OXYGEN STORAGE/TRANSPORT 22-JAN-04 1S6A TITLE THE X-RAY STRUCTURE OF THE CYANOBACTERIA SYNECHOCYSTIS TITLE 2 HEMOGLOBIN "CYANOGLOBIN" WITH AZIDE LIGAND 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 ORGANISM_COMMON: BACTERIA; SOURCE 4 STRAIN: PCC 6803; SOURCE 5 GENE: GLBN, SLR2097; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28C KEYWDS 2 ON 2 HELICAL FOLD, GLOBIN, HEME, IRON, HEMOGLOBIN, KEYWDS 2 CYANOBACTERIA, OXYGEN BINDING, HEXACOORDINATE, TRUNCATED EXPDTA X-RAY DIFFRACTION AUTHOR J.T.TRENT III,S.KUNDU,J.A.HOY,M.S.HARGROVE REVDAT 1 21-SEP-04 1S6A 0 JRNL AUTH J.T.TRENT III,S.KUNDU,J.A.HOY,M.S.HARGROVE JRNL TITL CRYSTALLOGRAPHIC ANALYSIS OF SYNECHOCYSTIS JRNL TITL 2 CYANOGLOBIN REVEALS THE STRUCTURAL CHANGES JRNL TITL 3 ACCOMPANYING LIGAND BINDING IN A HEXACOORDINATE JRNL TITL 4 HEMOGLOBIN. JRNL REF J.MOL.BIOL. V. 341 1097 2004 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.69 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.7 REMARK 3 NUMBER OF REFLECTIONS : 20036 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1080 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH : 1.69 REMARK 3 BIN RESOLUTION RANGE LOW : 1.73 REMARK 3 REFLECTION IN BIN (WORKING SET) : 244 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3880 REMARK 3 BIN FREE R VALUE SET COUNT : 15 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS : 1170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.75000 REMARK 3 B22 (A**2) : -0.75000 REMARK 3 B33 (A**2) : 1.49000 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): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.768 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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: NULL REMARK 4 REMARK 4 1S6A 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 RCSB021420. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-2003 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTAL VIEW REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34919 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 41.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 70.5 REMARK 200 DATA REDUNDANCY : 1.730 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 9.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.04 REMARK 200 R MERGE FOR SHELL (I) : 0.25700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: CYANIDE BOUND SYNECHOCYSTIS CYANOGLOBIN, PDB REMARK 200 ENTRY 1S69 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M SODIUM CITRATE, 20% SUCROSE, REMARK 280 50MM SODIUM AZIDE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,1/2+X,1/4+Z REMARK 290 3555 1/2-X,1/2-Y,1/2+Z REMARK 290 4555 1/2+Y,-X,3/4+Z REMARK 290 5555 1/2+X,1/2+Y,1/2+Z REMARK 290 6555 1/2-Y,1+X,3/4+Z REMARK 290 7555 1-X,1-Y,1+Z REMARK 290 8555 1+Y,1/2-X,5/4+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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 1.000000 0.000000 0.000000 41.67500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.29500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 41.67500 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 41.67500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.59000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.67500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 48.88500 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 41.67500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.67500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.59000 REMARK 290 SMTRY1 6 0.000000 -1.000000 0.000000 41.67500 REMARK 290 SMTRY2 6 1.000000 0.000000 0.000000 83.35000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.88500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 83.35000 REMARK 290 SMTRY2 7 0.000000 -1.000000 0.000000 83.35000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 65.18000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 83.35000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 41.67500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 81.47500 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 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 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 47 O HOH 138 1.93 REMARK 500 OD2 ASP A 37 O HOH 124 2.11 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1S69 RELATED DB: PDB DBREF 1S6A A 1 124 UNP P73925 GLBN_SYNY3 1 124 SEQRES 1 A 124 MET SER THR LEU TYR GLU LYS LEU GLY GLY THR THR ALA SEQRES 2 A 124 VAL ASP LEU ALA VAL ASP LYS PHE TYR GLU ARG VAL LEU SEQRES 3 A 124 GLN ASP ASP ARG ILE LYS HIS PHE PHE ALA ASP VAL ASP SEQRES 4 A 124 MET ALA LYS GLN ARG ALA HIS GLN LYS ALA PHE LEU THR SEQRES 5 A 124 TYR ALA PHE GLY GLY THR ASP LYS TYR ASP GLY ARG TYR SEQRES 6 A 124 MET ARG GLU ALA HIS LYS GLU LEU VAL GLU ASN HIS GLY SEQRES 7 A 124 LEU ASN GLY GLU HIS PHE ASP ALA VAL ALA GLU ASP LEU SEQRES 8 A 124 LEU ALA THR LEU LYS GLU MET GLY VAL PRO GLU ASP LEU SEQRES 9 A 124 ILE ALA GLU VAL ALA ALA VAL ALA GLY ALA PRO ALA HIS SEQRES 10 A 124 LYS ARG ASP VAL LEU ASN GLN HET FLC 227 13 HET AZI A 126 3 HET HEM A 125 43 HETNAM FLC CITRATE ANION HETNAM AZI AZIDE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 FLC C6 H5 O7 3- FORMUL 3 AZI N3 1- FORMUL 4 HEM C34 H32 FE N4 O4 FORMUL 5 HOH *142(H2 O) HELIX 1 1 THR A 3 GLY A 9 1 7 HELIX 2 2 GLY A 9 GLN A 27 1 19 HELIX 3 3 ILE A 31 ALA A 36 5 6 HELIX 4 4 ASP A 39 PHE A 55 1 17 HELIX 5 5 TYR A 65 GLY A 78 1 14 HELIX 6 6 ASN A 80 GLY A 99 1 20 HELIX 7 7 PRO A 101 ALA A 114 1 14 HELIX 8 8 ALA A 114 LEU A 122 1 9 LINK NE2 HIS A 70 FE HEM A 125 LINK NE2 HIS A 117 CAB HEM A 125 LINK N3 AZI A 126 FE HEM A 125 CRYST1 83.350 83.350 65.180 90.00 90.00 90.00 I 41 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 0.011998 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011998 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015342 0.00000