10 20 30 40 50 60 70 80 2DC3 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXYGEN STORAGE/TRANSPORT 21-DEC-05 2DC3
TITLE CRYSTAL STRUCTURE OF HUMAN CYTOGLOBIN AT 1.68 ANGSTROMS TITLE 2 RESOLUTION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOGLOBIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HISTOGLOBIN, HGB, STELLATE CELL ACTIVATION- COMPND 5 ASSOCIATED PROTEIN; COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: BACTERIA; SOURCE 6 GENE: CYGB; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS CYTOGLOBIN, MYOGLOBIN, HEME, OXYGEN TRANSPORT, OXYGEN KEYWDS 2 STORAGE, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, KEYWDS 3 RSGI, STRUCTURAL GENOMICS, OXYGEN STORAGE/TRANSPORT COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR M.MAKINO,H.SUGIMOTO,H.SAWAI,N.KAWADA,K.YOSHIZATO,Y.SHIRO, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 2 24-FEB-09 2DC3 1 VERSN REVDAT 1 23-MAY-06 2DC3 0
JRNL AUTH M.MAKINO,H.SUGIMOTO,H.SAWAI,N.KAWADA,K.YOSHIZATO, JRNL AUTH 2 Y.SHIRO JRNL TITL HIGH-RESOLUTION STRUCTURE OF HUMAN CYTOGLOBIN: JRNL TITL 2 IDENTIFICATION OF EXTRA N- AND C-TERMINI AND A NEW JRNL TITL 3 DIMERIZATION MODE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 62 671 2006 JRNL REFN ISSN 0907-4449 JRNL PMID 16699195 JRNL DOI 10.1107/S0907444906013813
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.68 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 37014 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) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1927 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.68 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2626 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.1280 REMARK 3 BIN FREE R VALUE SET COUNT : 135 REMARK 3 BIN FREE R VALUE : 0.2330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2771 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 269 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.67000 REMARK 3 B22 (A**2) : -0.23000 REMARK 3 B33 (A**2) : -0.46000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.30000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.143 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.090 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.377 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2951 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2656 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4039 ; 1.558 ; 2.042 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6168 ; 0.890 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 355 ; 4.677 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 129 ;32.060 ;23.643 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 490 ;13.768 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;21.240 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 422 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3279 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 586 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 745 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2695 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1478 ; 0.189 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1667 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 187 ; 0.182 ; 0.200 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): 21 ; 0.253 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 127 ; 0.236 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 30 ; 0.315 ; 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): 2270 ; 1.973 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 696 ; 0.605 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2849 ; 2.215 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1428 ; 3.516 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1186 ; 4.751 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6814 ; 2.259 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 265 ; 8.671 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5517 ; 2.638 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 2DC3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-DEC-05. REMARK 100 THE RCSB ID CODE IS RCSB025237.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45PX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39043 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.030 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1V5H REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4M SODIUM ACETATE, 100MM SODIUM REMARK 280 CACODYLATE, 5MM KCN, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 39.26500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.38000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.26500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.38000 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 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER.
REMARK 350 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1291 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1346 LIES ON A SPECIAL POSITION.
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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 LYS A 3 REMARK 465 VAL A 4 REMARK 465 PRO A 5 REMARK 465 GLY A 6 REMARK 465 GLU A 7 REMARK 465 MET A 8 REMARK 465 GLU A 9 REMARK 465 ILE A 10 REMARK 465 GLU A 11 REMARK 465 ARG A 12 REMARK 465 ARG A 13 REMARK 465 GLU A 14 REMARK 465 ARG A 15 REMARK 465 SER A 16 REMARK 465 GLY A 189 REMARK 465 PRO A 190 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 LYS B 3 REMARK 465 VAL B 172 REMARK 465 GLN B 173 REMARK 465 GLN B 174 REMARK 465 VAL B 175 REMARK 465 PRO B 176 REMARK 465 ASN B 177 REMARK 465 ALA B 178 REMARK 465 THR B 179 REMARK 465 THR B 180 REMARK 465 PRO B 181 REMARK 465 PRO B 182 REMARK 465 ALA B 183 REMARK 465 THR B 184 REMARK 465 LEU B 185 REMARK 465 PRO B 186 REMARK 465 SER B 187 REMARK 465 SER B 188 REMARK 465 GLY B 189 REMARK 465 PRO B 190
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 DISTANCE REMARK 500 O HOH B 227 O HOH B 307 1.39 REMARK 500 NZ LYS B 118 O HOH B 243 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 OE2 GLU B 7 O HOH A 1311 4555 1.15 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 24 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 149 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE B 143 45.38 -151.23 REMARK 500 PRO B 144 171.71 -56.64 REMARK 500 REMARK 500 REMARK: NULL
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 191 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 81 NE2 REMARK 620 2 HIS A 113 NE2 178.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 191 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 81 NE2 REMARK 620 2 HIS B 113 NE2 176.3 REMARK 620 N 1
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 191 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 191 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 1200
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MY_001000023.1 RELATED DB: TARGETDB
DBREF 2DC3 A 1 190 UNP Q8WWM9 CYGB_HUMAN 1 190 DBREF 2DC3 B 1 190 UNP Q8WWM9 CYGB_HUMAN 1 190
SEQADV 2DC3 GLY A -2 UNP Q8WWM9 CLONING ARTIFACT SEQADV 2DC3 SER A -1 UNP Q8WWM9 CLONING ARTIFACT SEQADV 2DC3 HIS A 0 UNP Q8WWM9 CLONING ARTIFACT SEQADV 2DC3 GLY B -2 UNP Q8WWM9 CLONING ARTIFACT SEQADV 2DC3 SER B -1 UNP Q8WWM9 CLONING ARTIFACT SEQADV 2DC3 HIS B 0 UNP Q8WWM9 CLONING ARTIFACT
SEQRES 1 A 193 GLY SER HIS MET GLU LYS VAL PRO GLY GLU MET GLU ILE SEQRES 2 A 193 GLU ARG ARG GLU ARG SER GLU GLU LEU SER GLU ALA GLU SEQRES 3 A 193 ARG LYS ALA VAL GLN ALA MET TRP ALA ARG LEU TYR ALA SEQRES 4 A 193 ASN CYS GLU ASP VAL GLY VAL ALA ILE LEU VAL ARG PHE SEQRES 5 A 193 PHE VAL ASN PHE PRO SER ALA LYS GLN TYR PHE SER GLN SEQRES 6 A 193 PHE LYS HIS MET GLU ASP PRO LEU GLU MET GLU ARG SER SEQRES 7 A 193 PRO GLN LEU ARG LYS HIS ALA CYS ARG VAL MET GLY ALA SEQRES 8 A 193 LEU ASN THR VAL VAL GLU ASN LEU HIS ASP PRO ASP LYS SEQRES 9 A 193 VAL SER SER VAL LEU ALA LEU VAL GLY LYS ALA HIS ALA SEQRES 10 A 193 LEU LYS HIS LYS VAL GLU PRO VAL TYR PHE LYS ILE LEU SEQRES 11 A 193 SER GLY VAL ILE LEU GLU VAL VAL ALA GLU GLU PHE ALA SEQRES 12 A 193 SER ASP PHE PRO PRO GLU THR GLN ARG ALA TRP ALA LYS SEQRES 13 A 193 LEU ARG GLY LEU ILE TYR SER HIS VAL THR ALA ALA TYR SEQRES 14 A 193 LYS GLU VAL GLY TRP VAL GLN GLN VAL PRO ASN ALA THR SEQRES 15 A 193 THR PRO PRO ALA THR LEU PRO SER SER GLY PRO SEQRES 1 B 193 GLY SER HIS MET GLU LYS VAL PRO GLY GLU MET GLU ILE SEQRES 2 B 193 GLU ARG ARG GLU ARG SER GLU GLU LEU SER GLU ALA GLU SEQRES 3 B 193 ARG LYS ALA VAL GLN ALA MET TRP ALA ARG LEU TYR ALA SEQRES 4 B 193 ASN CYS GLU ASP VAL GLY VAL ALA ILE LEU VAL ARG PHE SEQRES 5 B 193 PHE VAL ASN PHE PRO SER ALA LYS GLN TYR PHE SER GLN SEQRES 6 B 193 PHE LYS HIS MET GLU ASP PRO LEU GLU MET GLU ARG SER SEQRES 7 B 193 PRO GLN LEU ARG LYS HIS ALA CYS ARG VAL MET GLY ALA SEQRES 8 B 193 LEU ASN THR VAL VAL GLU ASN LEU HIS ASP PRO ASP LYS SEQRES 9 B 193 VAL SER SER VAL LEU ALA LEU VAL GLY LYS ALA HIS ALA SEQRES 10 B 193 LEU LYS HIS LYS VAL GLU PRO VAL TYR PHE LYS ILE LEU SEQRES 11 B 193 SER GLY VAL ILE LEU GLU VAL VAL ALA GLU GLU PHE ALA SEQRES 12 B 193 SER ASP PHE PRO PRO GLU THR GLN ARG ALA TRP ALA LYS SEQRES 13 B 193 LEU ARG GLY LEU ILE TYR SER HIS VAL THR ALA ALA TYR SEQRES 14 B 193 LYS GLU VAL GLY TRP VAL GLN GLN VAL PRO ASN ALA THR SEQRES 15 B 193 THR PRO PRO ALA THR LEU PRO SER SER GLY PRO
HET HEM A 191 43 HET HEM B 191 43 HET ACY A1200 4
HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM ACY ACETIC ACID
HETSYN HEM HEME
FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 ACY C2 H4 O2 FORMUL 6 HOH *265(H2 O)
HELIX 1 1 SER A 20 ALA A 36 1 17 HELIX 2 2 ASN A 37 PHE A 53 1 17 HELIX 3 3 PRO A 54 PHE A 60 5 7 HELIX 4 4 ASP A 68 GLU A 73 1 6 HELIX 5 5 SER A 75 ASN A 95 1 21 HELIX 6 6 ASP A 98 LYS A 116 1 19 HELIX 7 7 GLU A 120 PHE A 139 1 20 HELIX 8 8 ALA A 140 PHE A 143 5 4 HELIX 9 9 PRO A 144 VAL A 169 1 26 HELIX 10 10 GLY B 6 SER B 16 1 11 HELIX 11 11 SER B 20 ALA B 36 1 17 HELIX 12 12 ASN B 37 PHE B 53 1 17 HELIX 13 13 PRO B 54 PHE B 60 5 7 HELIX 14 14 ASP B 68 SER B 75 1 8 HELIX 15 15 SER B 75 ASN B 95 1 21 HELIX 16 16 ASP B 98 LYS B 116 1 19 HELIX 17 17 PRO B 121 PHE B 139 1 19 HELIX 18 18 PRO B 144 VAL B 169 1 26
SSBOND 1 CYS A 38 CYS B 83 1555 1555 2.06 SSBOND 2 CYS A 83 CYS B 38 1555 1555 2.04
LINK FE HEM A 191 NE2 HIS A 81 1555 1555 2.07 LINK FE HEM A 191 NE2 HIS A 113 1555 1555 2.07 LINK FE HEM B 191 NE2 HIS B 81 1555 1555 2.09 LINK FE HEM B 191 NE2 HIS B 113 1555 1555 2.06
CISPEP 1 VAL A 175 PRO A 176 0 -1.38
SITE 1 AC1 18 ALA A 56 TYR A 59 PHE A 60 GLN A 77 SITE 2 AC1 18 HIS A 81 ARG A 84 VAL A 85 HIS A 113 SITE 3 AC1 18 HIS A 117 VAL A 119 TYR A 123 PHE A 124 SITE 4 AC1 18 HOH A1212 HOH A1237 HOH A1314 HOH A1331 SITE 5 AC1 18 HOH A1340 HOH A1348 SITE 1 AC2 17 ALA B 56 TYR B 59 PHE B 60 GLN B 77 SITE 2 AC2 17 HIS B 81 VAL B 85 HIS B 113 HIS B 117 SITE 3 AC2 17 VAL B 119 PHE B 124 LEU B 127 HOH B 206 SITE 4 AC2 17 HOH B 219 HOH B 223 HOH B 226 HOH B 286 SITE 5 AC2 17 HOH B 296 SITE 1 AC3 8 TYR A 35 CYS A 83 GLY A 87 HOH A1211 SITE 2 AC3 8 HOH A1292 TYR B 35 CYS B 83 GLY B 87
CRYST1 78.530 52.760 83.440 90.00 87.75 90.00 C 1 2 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 0.012734 0.000000 -0.000500 0.00000
SCALE2 0.000000 0.018953 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011993 0.00000