10 20 30 40 50 60 70 80 4JM6 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 13-MAR-13 4JM6
TITLE CRYSTAL STRUCTURE OF CYTOCHROME C PEROXIDASE W191G-GATELESS IN COMPLEX TITLE 2 WITH 2,4-DIAMINOPYRIMIDINE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 72-362, DELETIONS G192-A193; COMPND 5 EC: 1.11.1.5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 285006; SOURCE 5 STRAIN: RM11-1A; SOURCE 6 GENE: CCP1 CCP CPO YKR066C, SCRG_04081; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)
KEYWDS MODEL SYSTEM, BULK SOLVENT, ORDERED WATERS, DOCKING, LIGAND BINDING, KEYWDS 2 FREE ENERGY CALCULATION, MOLECULAR DYNAMICS, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.E.BOYCE,M.FISCHER,I.FISH
REVDAT 3 20-NOV-13 4JM6 1 JRNL REVDAT 2 09-OCT-13 4JM6 1 JRNL REVDAT 1 01-MAY-13 4JM6 0
JRNL AUTH G.J.ROCKLIN,S.E.BOYCE,M.FISCHER,I.FISH,D.L.MOBLEY, JRNL AUTH 2 B.K.SHOICHET,K.A.DILL JRNL TITL BLIND PREDICTION OF CHARGED LIGAND BINDING AFFINITIES IN A JRNL TITL 2 MODEL BINDING SITE. JRNL REF J.MOL.BIOL. V. 425 4569 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23896298 JRNL DOI 10.1016/J.JMB.2013.07.030
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.BARELIER,S.E.BOYCE,M.FISCHER,I.FISH,D.B.GOODIN, REMARK 1 AUTH 2 B.K.SHOICHET REMARK 1 TITL DOCKING TO A WATER-FILLED MODEL BINDING SITE IN CYTOCHROME C REMARK 1 TITL 2 PEROXIDASE REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN
REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 72171 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) : 0.116 REMARK 3 R VALUE (WORKING SET) : 0.115 REMARK 3 FREE R VALUE : 0.145 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3644 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4376 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.1730 REMARK 3 BIN FREE R VALUE SET COUNT : 230 REMARK 3 BIN FREE R VALUE : 0.2150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2328 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 471 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.46000 REMARK 3 B22 (A**2) : 0.15000 REMARK 3 B33 (A**2) : -0.61000 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): 0.048 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.046 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.026 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.517 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2781 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1907 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3817 ; 1.741 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4657 ; 1.051 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 356 ; 5.978 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 145 ;35.107 ;25.103 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 477 ;13.180 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;26.789 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 360 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3280 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 590 ; 0.002 ; 0.020 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): 1616 ; 1.952 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 652 ; 0.770 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2634 ; 2.766 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1165 ; 4.299 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1175 ; 5.778 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4688 ; 1.840 ; 3.000 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 : 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 : 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 RIDING REMARK 3 POSITIONS U VALUES: REFINED INDIVIDUALLY
REMARK 4 REMARK 4 4JM6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAR-13. REMARK 100 THE RCSB ID CODE IS RCSB078220.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72171 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 61.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: APO CRYSTAL GROWN IN 500MM MES, PH REMARK 280 6.0. SOAKED INTO 50MM 2,4-DIAMINOPYRIMIDINE, 25% MPD PH 4.5 REMARK 280 (30MIN-1H), TEMPERATURE 283K
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 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.42300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.34650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.78750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.34650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.42300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.78750 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 DISTANCE REMARK 500 OE1 GLU A 265 O HOH A 607 2.17 REMARK 500 REMARK 500 REMARK: NULL 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),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 288 CD GLU A 288 OE1 -0.078 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 ASP A 34 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 155 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 160 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 165 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 MET A 228 CG - SD - CE ANGL. DEV. = -12.0 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 ALA A 192 31.02 -143.91 REMARK 500 ASP A 252 88.33 -155.10 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 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 575 O REMARK 620 2 HEM A 301 NA 84.9 REMARK 620 3 HEM A 301 NB 86.0 88.8 REMARK 620 4 HEM A 301 NC 91.0 175.8 90.8 REMARK 620 5 HEM A 301 ND 91.9 90.7 177.8 89.6 REMARK 620 6 HIS A 175 NE2 175.4 95.2 89.5 89.0 92.7 REMARK 620 N 1 2 3 4 5
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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LG3 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 304
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KXN RELATED DB: PDB REMARK 900 RELATED ID: 1KXM RELATED DB: PDB REMARK 900 RELATED ID: 4JM5 RELATED DB: PDB REMARK 900 RELATED ID: 4JM8 RELATED DB: PDB REMARK 900 RELATED ID: 4JM9 RELATED DB: PDB REMARK 900 RELATED ID: 4JMA RELATED DB: PDB REMARK 900 RELATED ID: 4JMW RELATED DB: PDB REMARK 900 RELATED ID: 4JPL RELATED DB: PDB REMARK 900 RELATED ID: 4JPT RELATED DB: PDB REMARK 900 RELATED ID: 4JPU RELATED DB: PDB REMARK 900 RELATED ID: 4JQJ RELATED DB: PDB REMARK 900 RELATED ID: 4JQK RELATED DB: PDB REMARK 900 RELATED ID: 4JQM RELATED DB: PDB REMARK 900 RELATED ID: 4JQN RELATED DB: PDB REMARK 900 RELATED ID: 4JMB RELATED DB: PDB REMARK 900 RELATED ID: 4JMS RELATED DB: PDB REMARK 900 RELATED ID: 4JMT RELATED DB: PDB REMARK 900 RELATED ID: 4JMV RELATED DB: PDB REMARK 900 RELATED ID: 4JMZ RELATED DB: PDB REMARK 900 RELATED ID: 4JN0 RELATED DB: PDB
DBREF 4JM6 A 4 292 UNP B3LRE1 B3LRE1_YEAS1 72 362
SEQADV 4JM6 GLY A 190 UNP B3LRE1 PRO 258 ENGINEERED MUTATION SEQADV 4JM6 GLY A 191 UNP B3LRE1 TRP 259 ENGINEERED MUTATION SEQADV 4JM6 A UNP B3LRE1 GLY 260 DELETION SEQADV 4JM6 A UNP B3LRE1 ALA 261 DELETION
SEQRES 1 A 289 LEU VAL HIS VAL ALA SER VAL GLU LYS GLY ARG SER TYR SEQRES 2 A 289 GLU ASP PHE GLN LYS VAL TYR ASN ALA ILE ALA LEU LYS SEQRES 3 A 289 LEU ARG GLU ASP ASP GLU TYR ASP ASN TYR ILE GLY TYR SEQRES 4 A 289 GLY PRO VAL LEU VAL ARG LEU ALA TRP HIS ILE SER GLY SEQRES 5 A 289 THR TRP ASP LYS HIS ASP ASN THR GLY GLY SER TYR GLY SEQRES 6 A 289 GLY THR TYR ARG PHE LYS LYS GLU PHE ASN ASP PRO SER SEQRES 7 A 289 ASN ALA GLY LEU GLN ASN GLY PHE LYS PHE LEU GLU PRO SEQRES 8 A 289 ILE HIS LYS GLU PHE PRO TRP ILE SER SER GLY ASP LEU SEQRES 9 A 289 PHE SER LEU GLY GLY VAL THR ALA VAL GLN GLU MET GLN SEQRES 10 A 289 GLY PRO LYS ILE PRO TRP ARG CYS GLY ARG VAL ASP THR SEQRES 11 A 289 PRO GLU ASP THR THR PRO ASP ASN GLY ARG LEU PRO ASP SEQRES 12 A 289 ALA ASP LYS ASP ALA GLY TYR VAL ARG THR PHE PHE GLN SEQRES 13 A 289 ARG LEU ASN MET ASN ASP ARG GLU VAL VAL ALA LEU MET SEQRES 14 A 289 GLY ALA HIS ALA LEU GLY LYS THR HIS LEU LYS ASN SER SEQRES 15 A 289 GLY TYR GLU GLY GLY GLY ALA ASN ASN VAL PHE THR ASN SEQRES 16 A 289 GLU PHE TYR LEU ASN LEU LEU ASN GLU ASP TRP LYS LEU SEQRES 17 A 289 GLU LYS ASN ASP ALA ASN ASN GLU GLN TRP ASP SER LYS SEQRES 18 A 289 SER GLY TYR MET MET LEU PRO THR ASP TYR SER LEU ILE SEQRES 19 A 289 GLN ASP PRO LYS TYR LEU SER ILE VAL LYS GLU TYR ALA SEQRES 20 A 289 ASN ASP GLN ASP LYS PHE PHE LYS ASP PHE SER LYS ALA SEQRES 21 A 289 PHE GLU LYS LEU LEU GLU ASN GLY ILE THR PHE PRO LYS SEQRES 22 A 289 ASP ALA PRO SER PRO PHE ILE PHE LYS THR LEU GLU GLU SEQRES 23 A 289 GLN GLY LEU
HET HEM A 301 43 HET LG3 A 302 16 HET PO4 A 303 5 HET PO4 A 304 5
HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM LG3 PYRIMIDINE-2,4-DIAMINE HETNAM PO4 PHOSPHATE ION
HETSYN HEM HEME
FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 LG3 C4 H6 N4 FORMUL 4 PO4 2(O4 P 3-) FORMUL 6 HOH *471(H2 O)
HELIX 1 1 SER A 15 ASP A 33 1 19 HELIX 2 2 GLU A 35 ILE A 40 1 6 HELIX 3 3 TYR A 42 GLY A 55 1 14 HELIX 4 4 GLY A 69 ARG A 72 5 4 HELIX 5 5 PHE A 73 ASN A 78 1 6 HELIX 6 6 ASP A 79 GLY A 84 5 6 HELIX 7 7 LEU A 85 PHE A 99 1 15 HELIX 8 8 SER A 103 MET A 119 1 17 HELIX 9 9 PRO A 134 THR A 138 5 5 HELIX 10 10 ASP A 150 ARG A 160 1 11 HELIX 11 11 ASN A 164 GLY A 173 1 10 HELIX 12 12 ALA A 174 LEU A 177 5 4 HELIX 13 13 HIS A 181 GLY A 186 1 6 HELIX 14 14 ASN A 198 GLU A 207 1 10 HELIX 15 15 LEU A 230 ASP A 239 1 10 HELIX 16 16 ASP A 239 ASN A 251 1 13 HELIX 17 17 ASP A 252 ASN A 270 1 19 HELIX 18 18 THR A 286 GLY A 291 1 6
SHEET 1 A 2 HIS A 6 VAL A 7 0 SHEET 2 A 2 ILE A 272 THR A 273 1 O THR A 273 N HIS A 6 SHEET 1 B 2 GLY A 178 THR A 180 0 SHEET 2 B 2 GLY A 189 ASN A 193 -1 O ASN A 193 N GLY A 178 SHEET 1 C 3 LYS A 210 LYS A 213 0 SHEET 2 C 3 GLU A 219 ASP A 222 -1 O ASP A 222 N LYS A 210 SHEET 3 C 3 MET A 228 MET A 229 -1 O MET A 229 N TRP A 221
LINK FE HEM A 301 O HOH A 575 1555 1555 2.02 LINK NE2 HIS A 175 FE HEM A 301 1555 1555 2.05
SITE 1 AC1 24 PRO A 44 ARG A 48 TRP A 51 PRO A 145 SITE 2 AC1 24 ASP A 146 ALA A 147 LEU A 171 MET A 172 SITE 3 AC1 24 ALA A 174 HIS A 175 LEU A 177 GLY A 178 SITE 4 AC1 24 LYS A 179 THR A 180 HIS A 181 ASN A 184 SITE 5 AC1 24 SER A 185 LEU A 230 THR A 232 LG3 A 302 SITE 6 AC1 24 HOH A 448 HOH A 461 HOH A 477 HOH A 575 SITE 1 AC2 7 HIS A 175 LEU A 177 GLY A 178 GLY A 190 SITE 2 AC2 7 MET A 228 ASP A 233 HEM A 301 SITE 1 AC3 4 LEU A 30 HOH A 409 HOH A 485 HOH A 796 SITE 1 AC4 2 TYR A 36 ASP A 37
CRYST1 50.846 75.575 106.693 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 0.019667 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013232 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009373 0.00000