HEADER OXIDOREDUCTASE 05-OCT-05 2B7R TITLE STRUCTURE OF E378D MUTANT FLAVOCYTOCHROME C3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FLAVOCYTOCHROME C3, FLAVOCYTOCHROME C, FCC3; COMPND 5 EC: 1.3.99.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA FRIGIDIMARINA; SOURCE 3 ORGANISM_TAXID: 56812; SOURCE 4 GENE: FCC; SOURCE 5 EXPRESSION_SYSTEM: SHEWANELLA FRIGIDIMARINA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 56812; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: EG301; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMMB503EH KEYWDS FLAVOCYTOCHROME C3, FUMARATE REDUCTASE, PROTON DELIVERY, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.L.PANKHURST,C.G.MOWAT,E.L.ROTHERY,C.S.MILES,M.D.WALKINSHAW, AUTHOR 2 G.A.REID,S.K.CHAPMAN REVDAT 6 15-NOV-23 2B7R 1 ATOM REVDAT 5 25-OCT-23 2B7R 1 REMARK REVDAT 4 10-NOV-21 2B7R 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2B7R 1 VERSN REVDAT 2 01-AUG-06 2B7R 1 JRNL REVDAT 1 23-MAY-06 2B7R 0 JRNL AUTH K.L.PANKHURST,C.G.MOWAT,E.L.ROTHERY,J.M.HUDSON,A.K.JONES, JRNL AUTH 2 C.S.MILES,M.D.WALKINSHAW,F.A.ARMSTRONG,G.A.REID,S.K.CHAPMAN JRNL TITL A PROTON DELIVERY PATHWAY IN THE SOLUBLE FUMARATE REDUCTASE JRNL TITL 2 FROM SHEWANELLA FRIGIDIMARINA. JRNL REF J.BIOL.CHEM. V. 281 20589 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16699170 JRNL DOI 10.1074/JBC.M603077200 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 68525 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3629 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4638 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.1790 REMARK 3 BIN FREE R VALUE SET COUNT : 234 REMARK 3 BIN FREE R VALUE : 0.2190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4176 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 234 REMARK 3 SOLVENT ATOMS : 1084 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.71000 REMARK 3 B22 (A**2) : 0.40000 REMARK 3 B33 (A**2) : -1.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.093 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.466 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4511 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6171 ; 1.314 ; 2.073 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 567 ; 5.579 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;34.491 ;25.029 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 697 ;11.902 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.873 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 656 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3438 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1796 ; 0.226 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2996 ; 0.283 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 577 ; 0.114 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.035 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 18 ; 0.118 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.116 ; 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): 2792 ; 0.561 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4441 ; 1.009 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1851 ; 1.772 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1730 ; 2.742 ; 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): 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 : 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 2B7R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-SEP-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 72178 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.900 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: 1QJD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRISHCL, 80MM NACL, 10MM NA REMARK 280 FUMARATE, 15% PEG8000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K, PH 8 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,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 46.43950 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 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 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 LYS A 569 REMARK 465 LYS A 570 REMARK 465 ASN A 571 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 ASP A 21 CB CG OD1 OD2 REMARK 470 GLU A 23 CD OE1 OE2 REMARK 470 GLU A 48 CD OE1 OE2 REMARK 470 ASP A 101 CB CG OD1 OD2 REMARK 470 LYS A 110 CG CD CE NZ REMARK 470 LYS A 112 CB CG CD CE NZ REMARK 470 LYS A 184 CD CE NZ REMARK 470 LYS A 415 CE NZ REMARK 470 LYS A 476 CD CE NZ REMARK 470 GLU A 481 CG CD OE1 OE2 REMARK 470 LYS A 515 NZ REMARK 470 LYS A 522 CD CE NZ REMARK 470 LYS A 523 NZ 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 ALA A 169 O HOH A 2598 1.96 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 2 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 378 CB - CG - OD2 ANGL. DEV. = 5.5 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 ASP A 111 36.22 -90.72 REMARK 500 THR A 248 127.74 -36.21 REMARK 500 ASP A 271 99.88 -69.18 REMARK 500 PHE A 395 -6.88 -148.43 REMARK 500 ASN A 490 15.12 -150.33 REMARK 500 HIS A 504 -49.29 -132.35 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 802 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 8 NE2 REMARK 620 2 HEM A 802 NA 89.6 REMARK 620 3 HEM A 802 NB 93.4 90.4 REMARK 620 4 HEM A 802 NC 94.2 176.1 88.7 REMARK 620 5 HEM A 802 ND 88.4 89.3 178.2 91.5 REMARK 620 6 HIS A 40 NE2 175.6 86.1 87.8 90.1 90.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 801 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 18 NE2 REMARK 620 2 HEM A 801 NA 91.9 REMARK 620 3 HEM A 801 NB 89.3 91.5 REMARK 620 4 HEM A 801 NC 84.3 176.1 87.7 REMARK 620 5 HEM A 801 ND 87.7 89.1 176.9 91.4 REMARK 620 6 HIS A 75 NE2 178.0 87.2 88.9 96.6 94.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 803 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 58 NE2 REMARK 620 2 HEM A 803 NA 91.5 REMARK 620 3 HEM A 803 NB 91.9 92.3 REMARK 620 4 HEM A 803 NC 90.6 177.1 89.6 REMARK 620 5 HEM A 803 ND 91.8 88.2 176.3 89.7 REMARK 620 6 HIS A 72 NE2 176.2 90.8 85.1 87.2 91.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 804 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 61 NE2 REMARK 620 2 HEM A 804 NA 91.0 REMARK 620 3 HEM A 804 NB 93.1 89.5 REMARK 620 4 HEM A 804 NC 91.5 177.4 90.7 REMARK 620 5 HEM A 804 ND 90.3 89.7 176.5 90.0 REMARK 620 6 HIS A 86 NE2 178.4 89.2 88.5 88.3 88.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1810 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 506 O REMARK 620 2 MET A 507 O 85.9 REMARK 620 3 GLY A 508 O 86.1 76.0 REMARK 620 4 GLU A 534 O 102.7 171.2 102.6 REMARK 620 5 THR A 536 O 163.9 78.5 86.3 92.8 REMARK 620 6 HOH A1865 O 84.7 84.0 158.6 98.3 97.4 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 NA A 1810 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 1805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FUM A 1806 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QJD RELATED DB: PDB REMARK 900 WILD-TYPE ENZYME REMARK 900 RELATED ID: 2B7S RELATED DB: PDB REMARK 900 THE SAME PROTEIN, R381K MUTANT DBREF 2B7R A 1 571 UNP Q02469 FRDA_SHEFR 26 596 SEQADV 2B7R ASP A 378 UNP Q02469 GLU 403 ENGINEERED MUTATION SEQRES 1 A 571 ALA ASP ASN LEU ALA GLU PHE HIS VAL GLN ASN GLN GLU SEQRES 2 A 571 CYS ASP SER CYS HIS THR PRO ASP GLY GLU LEU SER ASN SEQRES 3 A 571 ASP SER LEU THR TYR GLU ASN THR GLN CYS VAL SER CYS SEQRES 4 A 571 HIS GLY THR LEU ALA GLU VAL ALA GLU THR THR LYS HIS SEQRES 5 A 571 GLU HIS TYR ASN ALA HIS ALA SER HIS PHE PRO GLY GLU SEQRES 6 A 571 VAL ALA CYS THR SER CYS HIS SER ALA HIS GLU LYS SER SEQRES 7 A 571 MET VAL TYR CYS ASP SER CYS HIS SER PHE ASP PHE ASN SEQRES 8 A 571 MET PRO TYR ALA LYS LYS TRP LEU ARG ASP GLU PRO THR SEQRES 9 A 571 ILE ALA GLU LEU ALA LYS ASP LYS SER GLU ARG GLN ALA SEQRES 10 A 571 ALA LEU ALA SER ALA PRO HIS ASP THR VAL ASP VAL VAL SEQRES 11 A 571 VAL VAL GLY SER GLY GLY ALA GLY PHE SER ALA ALA ILE SEQRES 12 A 571 SER ALA THR ASP SER GLY ALA LYS VAL ILE LEU ILE GLU SEQRES 13 A 571 LYS GLU PRO VAL ILE GLY GLY ASN ALA LYS LEU ALA ALA SEQRES 14 A 571 GLY GLY MET ASN ALA ALA TRP THR ASP GLN GLN LYS ALA SEQRES 15 A 571 LYS LYS ILE THR ASP SER PRO GLU LEU MET PHE GLU ASP SEQRES 16 A 571 THR MET LYS GLY GLY GLN ASN ILE ASN ASP PRO ALA LEU SEQRES 17 A 571 VAL LYS VAL LEU SER SER HIS SER LYS ASP SER VAL ASP SEQRES 18 A 571 TRP MET THR ALA MET GLY ALA ASP LEU THR ASP VAL GLY SEQRES 19 A 571 MET MET GLY GLY ALA SER VAL ASN ARG ALA HIS ARG PRO SEQRES 20 A 571 THR GLY GLY ALA GLY VAL GLY ALA HIS VAL VAL GLN VAL SEQRES 21 A 571 LEU TYR ASP ASN ALA VAL LYS ARG ASN ILE ASP LEU ARG SEQRES 22 A 571 MET ASN THR ARG GLY ILE GLU VAL LEU LYS ASP ASP LYS SEQRES 23 A 571 GLY THR VAL LYS GLY ILE LEU VAL LYS GLY MET TYR LYS SEQRES 24 A 571 GLY TYR TYR TRP VAL LYS ALA ASP ALA VAL ILE LEU ALA SEQRES 25 A 571 THR GLY GLY PHE ALA LYS ASN ASN GLU ARG VAL ALA LYS SEQRES 26 A 571 LEU ASP PRO SER LEU LYS GLY PHE ILE SER THR ASN GLN SEQRES 27 A 571 PRO GLY ALA VAL GLY ASP GLY LEU ASP VAL ALA GLU ASN SEQRES 28 A 571 ALA GLY GLY ALA LEU LYS ASP MET GLN TYR ILE GLN ALA SEQRES 29 A 571 HIS PRO THR LEU SER VAL LYS GLY GLY VAL MET VAL THR SEQRES 30 A 571 ASP ALA VAL ARG GLY ASN GLY ALA ILE LEU VAL ASN ARG SEQRES 31 A 571 GLU GLY LYS ARG PHE VAL ASN GLU ILE THR THR ARG ASP SEQRES 32 A 571 LYS ALA SER ALA ALA ILE LEU ALA GLN THR GLY LYS SER SEQRES 33 A 571 ALA TYR LEU ILE PHE ASP ASP SER VAL ARG LYS SER LEU SEQRES 34 A 571 SER LYS ILE ASP LYS TYR ILE GLY LEU GLY VAL ALA PRO SEQRES 35 A 571 THR ALA ASP SER LEU VAL LYS LEU GLY LYS MET GLU GLY SEQRES 36 A 571 ILE ASP GLY LYS ALA LEU THR GLU THR VAL ALA ARG TYR SEQRES 37 A 571 ASN SER LEU VAL SER SER GLY LYS ASP THR ASP PHE GLU SEQRES 38 A 571 ARG PRO ASN LEU PRO ARG ALA LEU ASN GLU GLY ASN TYR SEQRES 39 A 571 TYR ALA ILE GLU VAL THR PRO GLY VAL HIS HIS THR MET SEQRES 40 A 571 GLY GLY VAL MET ILE ASP THR LYS ALA GLU VAL MET ASN SEQRES 41 A 571 ALA LYS LYS GLN VAL ILE PRO GLY LEU TYR GLY ALA GLY SEQRES 42 A 571 GLU VAL THR GLY GLY VAL HIS GLY ALA ASN ARG LEU GLY SEQRES 43 A 571 GLY ASN ALA ILE SER ASP ILE ILE THR PHE GLY ARG LEU SEQRES 44 A 571 ALA GLY GLU GLU ALA ALA LYS TYR SER LYS LYS ASN HET NA A1810 1 HET HEM A 801 43 HET HEM A 802 43 HET HEM A 803 43 HET HEM A 804 43 HET FAD A1805 53 HET FUM A1806 8 HETNAM NA SODIUM ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM FUM FUMARIC ACID HETSYN HEM HEME FORMUL 2 NA NA 1+ FORMUL 3 HEM 4(C34 H32 FE N4 O4) FORMUL 7 FAD C27 H33 N9 O15 P2 FORMUL 8 FUM C4 H4 O4 FORMUL 9 HOH *1084(H2 O) HELIX 1 1 ASN A 3 GLN A 10 1 8 HELIX 2 2 GLU A 13 CYS A 17 5 5 HELIX 3 3 LEU A 29 GLY A 41 1 13 HELIX 4 4 THR A 42 GLU A 48 1 7 HELIX 5 5 ALA A 67 CYS A 71 5 5 HELIX 6 6 VAL A 80 CYS A 85 5 6 HELIX 7 7 ALA A 106 LYS A 110 5 5 HELIX 8 8 ASP A 111 SER A 121 1 11 HELIX 9 9 GLY A 135 SER A 148 1 14 HELIX 10 10 ASN A 164 ALA A 168 5 5 HELIX 11 11 THR A 177 LYS A 183 1 7 HELIX 12 12 SER A 188 GLY A 200 1 13 HELIX 13 13 ASP A 205 MET A 226 1 22 HELIX 14 14 GLY A 252 ARG A 268 1 17 HELIX 15 15 ASN A 319 ASP A 327 1 9 HELIX 16 16 PRO A 328 LYS A 331 5 4 HELIX 17 17 GLY A 343 ALA A 352 1 10 HELIX 18 18 ASP A 378 ASN A 383 1 6 HELIX 19 19 THR A 401 ALA A 411 1 11 HELIX 20 20 GLN A 412 SER A 416 5 5 HELIX 21 21 ASP A 423 LEU A 429 1 7 HELIX 22 22 SER A 430 GLY A 439 1 10 HELIX 23 23 SER A 446 GLY A 455 1 10 HELIX 24 24 ASP A 457 GLY A 475 1 19 HELIX 25 25 GLY A 547 SER A 568 1 22 SHEET 1 A 4 ASP A 125 THR A 126 0 SHEET 2 A 4 GLY A 300 LYS A 305 1 O LYS A 305 N ASP A 125 SHEET 3 A 4 VAL A 289 GLY A 296 -1 N VAL A 294 O TYR A 302 SHEET 4 A 4 THR A 276 LYS A 283 -1 N LEU A 282 O LYS A 290 SHEET 1 B 6 ASP A 271 ARG A 273 0 SHEET 2 B 6 VAL A 152 ILE A 155 1 N LEU A 154 O ASP A 271 SHEET 3 B 6 VAL A 129 VAL A 132 1 N VAL A 131 O ILE A 153 SHEET 4 B 6 ALA A 308 LEU A 311 1 O ILE A 310 N VAL A 132 SHEET 5 B 6 VAL A 525 GLY A 531 1 O TYR A 530 N LEU A 311 SHEET 6 B 6 GLU A 517 MET A 519 -1 N VAL A 518 O ILE A 526 SHEET 1 C 3 MET A 172 ASN A 173 0 SHEET 2 C 3 ALA A 244 ARG A 246 -1 O HIS A 245 N MET A 172 SHEET 3 C 3 ASP A 232 GLY A 234 -1 N ASP A 232 O ARG A 246 SHEET 1 D 3 LEU A 356 LYS A 357 0 SHEET 2 D 3 GLY A 509 MET A 511 -1 O GLY A 509 N LYS A 357 SHEET 3 D 3 THR A 536 GLY A 537 1 O GLY A 537 N VAL A 510 SHEET 1 E 4 ILE A 362 SER A 369 0 SHEET 2 E 4 TYR A 494 THR A 506 -1 O HIS A 505 N GLN A 363 SHEET 3 E 4 ALA A 417 ASP A 422 -1 N ALA A 417 O VAL A 499 SHEET 4 E 4 ILE A 386 VAL A 388 -1 N VAL A 388 O TYR A 418 SHEET 1 F 3 ILE A 362 SER A 369 0 SHEET 2 F 3 TYR A 494 THR A 506 -1 O HIS A 505 N GLN A 363 SHEET 3 F 3 THR A 443 ALA A 444 -1 N ALA A 444 O TYR A 494 LINK SG CYS A 14 CAB HEM A 801 1555 1555 2.12 LINK SG CYS A 17 CAC HEM A 801 1555 1555 2.28 LINK SG CYS A 36 CAB HEM A 802 1555 1555 1.97 LINK SG CYS A 39 CAC HEM A 802 1555 1555 2.68 LINK SG CYS A 68 CAB HEM A 803 1555 1555 2.01 LINK SG CYS A 71 CAC HEM A 803 1555 1555 2.23 LINK SG CYS A 82 CAB HEM A 804 1555 1555 2.03 LINK SG CYS A 85 CAC HEM A 804 1555 1555 2.36 LINK NE2 HIS A 8 FE HEM A 802 1555 1555 2.14 LINK NE2 HIS A 18 FE HEM A 801 1555 1555 2.15 LINK NE2 HIS A 40 FE HEM A 802 1555 1555 2.10 LINK NE2 HIS A 58 FE HEM A 803 1555 1555 2.12 LINK NE2 HIS A 61 FE HEM A 804 1555 1555 2.09 LINK NE2 HIS A 72 FE HEM A 803 1555 1555 2.15 LINK NE2 HIS A 75 FE HEM A 801 1555 1555 2.13 LINK NE2 HIS A 86 FE HEM A 804 1555 1555 2.14 LINK O THR A 506 NA NA A1810 1555 1555 2.47 LINK O MET A 507 NA NA A1810 1555 1555 2.99 LINK O GLY A 508 NA NA A1810 1555 1555 2.47 LINK O GLU A 534 NA NA A1810 1555 1555 2.42 LINK O THR A 536 NA NA A1810 1555 1555 2.40 LINK NA NA A1810 O HOH A1865 1555 1555 2.36 CISPEP 1 ALA A 175 TRP A 176 0 -9.22 SITE 1 AC1 6 THR A 506 MET A 507 GLY A 508 GLU A 534 SITE 2 AC1 6 THR A 536 HOH A1865 SITE 1 AC2 12 CYS A 14 CYS A 17 HIS A 18 SER A 73 SITE 2 AC2 12 ALA A 74 HIS A 75 HOH A2017 HOH A2022 SITE 3 AC2 12 HOH A2068 HOH A2272 HOH A2799 HOH A2800 SITE 1 AC3 13 LEU A 4 PHE A 7 HIS A 8 GLN A 12 SITE 2 AC3 13 SER A 16 CYS A 36 CYS A 39 HIS A 40 SITE 3 AC3 13 HIS A 72 TYR A 94 HOH A2277 HOH A2506 SITE 4 AC3 13 HOH A2645 SITE 1 AC4 17 HIS A 40 LEU A 43 HIS A 52 ALA A 57 SITE 2 AC4 17 HIS A 58 VAL A 66 ALA A 67 CYS A 68 SITE 3 AC4 17 CYS A 71 HIS A 72 PHE A 90 ASN A 91 SITE 4 AC4 17 MET A 92 HEM A 804 HOH A1890 HOH A2251 SITE 5 AC4 17 HOH A2827 SITE 1 AC5 24 HIS A 54 ASN A 56 SER A 60 HIS A 61 SITE 2 AC5 24 CYS A 82 SER A 84 CYS A 85 HIS A 86 SITE 3 AC5 24 PHE A 88 LEU A 167 GLN A 338 VAL A 374 SITE 4 AC5 24 LYS A 431 LYS A 434 HEM A 803 HOH A1815 SITE 5 AC5 24 HOH A1830 HOH A1850 HOH A1885 HOH A1989 SITE 6 AC5 24 HOH A2004 HOH A2012 HOH A2302 HOH A2332 SITE 1 AC6 42 VAL A 132 GLY A 133 GLY A 135 GLY A 136 SITE 2 AC6 42 ALA A 137 GLU A 156 LYS A 157 GLU A 158 SITE 3 AC6 42 GLY A 162 GLY A 163 ASN A 164 ALA A 165 SITE 4 AC6 42 LEU A 167 ALA A 168 ALA A 169 GLY A 170 SITE 5 AC6 42 GLY A 171 ARG A 277 GLY A 278 ALA A 312 SITE 6 AC6 42 THR A 313 GLY A 314 THR A 336 GLN A 338 SITE 7 AC6 42 ASP A 344 MET A 375 HIS A 504 HIS A 505 SITE 8 AC6 42 GLY A 533 GLU A 534 ARG A 544 GLY A 547 SITE 9 AC6 42 ASN A 548 ALA A 549 ILE A 550 ILE A 553 SITE 10 AC6 42 FUM A1806 HOH A1814 HOH A1817 HOH A1818 SITE 11 AC6 42 HOH A1819 HOH A1844 SITE 1 AC7 10 GLY A 170 HIS A 365 THR A 377 ASP A 378 SITE 2 AC7 10 ARG A 402 HIS A 504 ARG A 544 GLY A 546 SITE 3 AC7 10 GLY A 547 FAD A1805 CRYST1 45.961 92.879 79.486 90.00 91.17 90.00 P 1 21 1 2 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 0.021758 0.000000 0.000444 0.00000 SCALE2 0.000000 0.010767 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012583 0.00000