HEADER OXIDOREDUCTASE 04-MAR-15 4YKF TITLE CRYSTAL STRUCTURE OF THE ALKYLHYDROPEROXIDE REDUCTASE SUBUNIT F (AHPF) TITLE 2 WITH NADH FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALKYL HYDROPEROXIDE REDUCTASE SUBUNIT F; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALKYL HYDROPEROXIDE REDUCTASE F52A PROTEIN; COMPND 5 EC: 1.8.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: AHPF, B0606, JW0599; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA GAMI 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.KAMARIAH,M.S.S.MANIMEKALAI,G.GRUBER,F.EISENHABER,B.EISENHABER REVDAT 2 08-NOV-23 4YKF 1 SOURCE JRNL REMARK LINK REVDAT 1 15-JUL-15 4YKF 0 JRNL AUTH N.KAMARIAH,M.S.S.MANIMEKALAI,W.NARTEY,F.EISENHABER, JRNL AUTH 2 B.EISENHABER,G.GRUBER JRNL TITL CRYSTALLOGRAPHIC AND SOLUTION STUDIES OF NAD(+)- AND JRNL TITL 2 NADH-BOUND ALKYLHYDROPEROXIDE REDUCTASE SUBUNIT F (AHPF) JRNL TITL 3 FROM ESCHERICHIA COLI PROVIDE INSIGHT INTO SEQUENTIAL JRNL TITL 4 ENZYMATIC STEPS JRNL REF BIOCHIM.BIOPHYS.ACTA V.1847 1139 2015 JRNL REFN ISSN 0006-3002 JRNL PMID 26092085 JRNL DOI 10.1016/J.BBABIO.2015.06.011 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.DIP,N.KAMARIAH,M.S.S.MANIMEKALAI,W.NARTEY, REMARK 1 AUTH 2 A.M.BALAKRISHNA,F.EISENHABER,B.EISENHABER,G.GRUBER REMARK 1 TITL STRUCTURE, MECHANISM AND ENSEMBLE FORMATION OF THE REMARK 1 TITL 2 ALKYLHYDROPEROXIDE REDUCTASE SUBUNITS AHPC AND AHPF FROM REMARK 1 TITL 3 ESCHERICHIA COLI REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 70 2848 2014 REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 25372677 REMARK 1 DOI 10.1107/S1399004714019233 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 21672 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1168 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1463 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3947 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 187 REMARK 3 SOLVENT ATOMS : 142 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.46000 REMARK 3 B22 (A**2) : -2.93000 REMARK 3 B33 (A**2) : 2.49000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.37000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.571 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.335 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.211 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.838 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.892 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.833 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4189 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4022 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5680 ; 1.676 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9268 ; 0.818 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 520 ; 7.247 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 168 ;36.565 ;25.119 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 707 ;17.700 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;15.741 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 658 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4854 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 863 ; 0.001 ; 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): 2083 ; 2.084 ; 3.092 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2082 ; 2.081 ; 3.091 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2602 ; 3.345 ; 4.632 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 521 REMARK 3 ORIGIN FOR THE GROUP (A): -25.5586 59.3634 142.0154 REMARK 3 T TENSOR REMARK 3 T11: 0.0565 T22: 0.0735 REMARK 3 T33: 0.1027 T12: -0.0012 REMARK 3 T13: -0.0423 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.0039 L22: 0.0851 REMARK 3 L33: 0.3041 L12: -0.0122 REMARK 3 L13: -0.0109 L23: 0.0299 REMARK 3 S TENSOR REMARK 3 S11: 0.0113 S12: -0.0126 S13: -0.0075 REMARK 3 S21: -0.0675 S22: 0.0194 S23: 0.0522 REMARK 3 S31: -0.0437 S32: -0.0245 S33: -0.0307 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 4 REMARK 4 4YKF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207598. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 0.1.26 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22917 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 49.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.31300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 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: 4O5Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA-HEPES, 2.5 % (V/V) PEG 400, 2 REMARK 280 M AMMONIUM SULFATE, 10 MM CADMIUM CHLORIDE, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 53.54500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.69500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.54500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.69500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -266.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -25.38837 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 339.08979 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 A 716 LIES ON A SPECIAL POSITION. 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 210 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 432 NE - CZ - NH1 ANGL. DEV. = 3.1 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 28 -167.36 -102.02 REMARK 500 SER A 57 74.40 -109.81 REMARK 500 ARG A 61 141.34 -38.62 REMARK 500 LEU A 83 -148.25 -103.82 REMARK 500 CYS A 129 97.75 -66.38 REMARK 500 PHE A 159 64.42 -100.49 REMARK 500 ASN A 167 40.61 37.76 REMARK 500 ASN A 177 49.25 32.57 REMARK 500 ALA A 204 -71.66 -36.00 REMARK 500 ARG A 244 107.16 -160.04 REMARK 500 VAL A 253 -88.90 -104.80 REMARK 500 SER A 260 -19.87 85.68 REMARK 500 ASP A 283 96.61 -64.82 REMARK 500 GLU A 299 -18.59 -46.40 REMARK 500 THR A 339 -0.49 68.42 REMARK 500 LYS A 519 -66.07 -151.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 202 ALA A 203 125.87 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 CD A 603 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 85 NE2 REMARK 620 2 GLU A 110 OE1 66.7 REMARK 620 3 GLU A 110 OE2 65.0 3.1 REMARK 620 4 HIS A 130 ND1 85.9 35.4 34.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAI A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 611 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 612 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 613 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 614 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 615 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 616 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 617 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 618 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 619 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YKG RELATED DB: PDB DBREF 4YKF A 1 521 UNP P35340 AHPF_ECOLI 1 521 SEQRES 1 A 521 MET LEU ASP THR ASN MET LYS THR GLN LEU LYS ALA TYR SEQRES 2 A 521 LEU GLU LYS LEU THR LYS PRO VAL GLU LEU ILE ALA THR SEQRES 3 A 521 LEU ASP ASP SER ALA LYS SER ALA GLU ILE LYS GLU LEU SEQRES 4 A 521 LEU ALA GLU ILE ALA GLU LEU SER ASP LYS VAL THR PHE SEQRES 5 A 521 LYS GLU ASP ASN SER LEU PRO VAL ARG LYS PRO SER PHE SEQRES 6 A 521 LEU ILE THR ASN PRO GLY SER ASN GLN GLY PRO ARG PHE SEQRES 7 A 521 ALA GLY SER PRO LEU GLY HIS GLU PHE THR SER LEU VAL SEQRES 8 A 521 LEU ALA LEU LEU TRP THR GLY GLY HIS PRO SER LYS GLU SEQRES 9 A 521 ALA GLN SER LEU LEU GLU GLN ILE ARG HIS ILE ASP GLY SEQRES 10 A 521 ASP PHE GLU PHE GLU THR TYR TYR SER LEU SER CYS HIS SEQRES 11 A 521 ASN CYS PRO ASP VAL VAL GLN ALA LEU ASN LEU MET SER SEQRES 12 A 521 VAL LEU ASN PRO ARG ILE LYS HIS THR ALA ILE ASP GLY SEQRES 13 A 521 GLY THR PHE GLN ASN GLU ILE THR ASP ARG ASN VAL MET SEQRES 14 A 521 GLY VAL PRO ALA VAL PHE VAL ASN GLY LYS GLU PHE GLY SEQRES 15 A 521 GLN GLY ARG MET THR LEU THR GLU ILE VAL ALA LYS ILE SEQRES 16 A 521 ASP THR GLY ALA GLU LYS ARG ALA ALA GLU GLU LEU ASN SEQRES 17 A 521 LYS ARG ASP ALA TYR ASP VAL LEU ILE VAL GLY SER GLY SEQRES 18 A 521 PRO ALA GLY ALA ALA ALA ALA ILE TYR SER ALA ARG LYS SEQRES 19 A 521 GLY ILE ARG THR GLY LEU MET GLY GLU ARG PHE GLY GLY SEQRES 20 A 521 GLN ILE LEU ASP THR VAL ASP ILE GLU ASN TYR ILE SER SEQRES 21 A 521 VAL PRO LYS THR GLU GLY GLN LYS LEU ALA GLY ALA LEU SEQRES 22 A 521 LYS VAL HIS VAL ASP GLU TYR ASP VAL ASP VAL ILE ASP SEQRES 23 A 521 SER GLN SER ALA SER LYS LEU ILE PRO ALA ALA VAL GLU SEQRES 24 A 521 GLY GLY LEU HIS GLN ILE GLU THR ALA SER GLY ALA VAL SEQRES 25 A 521 LEU LYS ALA ARG SER ILE ILE VAL ALA THR GLY ALA LYS SEQRES 26 A 521 TRP ARG ASN MET ASN VAL PRO GLY GLU ASP GLN TYR ARG SEQRES 27 A 521 THR LYS GLY VAL THR TYR CYS PRO HIS CYS ASP GLY PRO SEQRES 28 A 521 LEU PHE LYS GLY LYS ARG VAL ALA VAL ILE GLY GLY GLY SEQRES 29 A 521 ASN SER GLY VAL GLU ALA ALA ILE ASP LEU ALA GLY ILE SEQRES 30 A 521 VAL GLU HIS VAL THR LEU LEU GLU PHE ALA PRO GLU MET SEQRES 31 A 521 LYS ALA ASP GLN VAL LEU GLN ASP LYS LEU ARG SER LEU SEQRES 32 A 521 LYS ASN VAL ASP ILE ILE LEU ASN ALA GLN THR THR GLU SEQRES 33 A 521 VAL LYS GLY ASP GLY SER LYS VAL VAL GLY LEU GLU TYR SEQRES 34 A 521 ARG ASP ARG VAL SER GLY ASP ILE HIS ASN ILE GLU LEU SEQRES 35 A 521 ALA GLY ILE PHE VAL GLN ILE GLY LEU LEU PRO ASN THR SEQRES 36 A 521 ASN TRP LEU GLU GLY ALA VAL GLU ARG ASN ARG MET GLY SEQRES 37 A 521 GLU ILE ILE ILE ASP ALA LYS CYS GLU THR ASN VAL LYS SEQRES 38 A 521 GLY VAL PHE ALA ALA GLY ASP CYS THR THR VAL PRO TYR SEQRES 39 A 521 LYS GLN ILE ILE ILE ALA THR GLY GLU GLY ALA LYS ALA SEQRES 40 A 521 SER LEU SER ALA PHE ASP TYR LEU ILE ARG THR LYS THR SEQRES 41 A 521 ALA HET FAD A 601 53 HET NAI A 602 44 HET CD A 603 1 HET SO4 A 604 5 HET SO4 A 605 5 HET SO4 A 606 5 HET SO4 A 607 5 HET SO4 A 608 5 HET SO4 A 609 5 HET SO4 A 610 5 HET SO4 A 611 5 HET SO4 A 612 5 HET SO4 A 613 5 HET GOL A 614 6 HET GOL A 615 6 HET GOL A 616 6 HET PEG A 617 7 HET PEG A 618 7 HET PEG A 619 7 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETNAM CD CADMIUM ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN NAI NADH HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 NAI C21 H29 N7 O14 P2 FORMUL 4 CD CD 2+ FORMUL 5 SO4 10(O4 S 2-) FORMUL 15 GOL 3(C3 H8 O3) FORMUL 18 PEG 3(C4 H10 O3) FORMUL 21 HOH *142(H2 O) HELIX 1 AA1 ASP A 3 GLU A 15 1 13 HELIX 2 AA2 SER A 30 GLU A 45 1 16 HELIX 3 AA3 LEU A 83 HIS A 85 5 3 HELIX 4 AA4 GLU A 86 GLY A 98 1 13 HELIX 5 AA5 ALA A 105 HIS A 114 1 10 HELIX 6 AA6 ASN A 131 ASN A 146 1 16 HELIX 7 AA7 PHE A 159 ARG A 166 1 8 HELIX 8 AA8 THR A 187 ASP A 196 1 10 HELIX 9 AA9 ALA A 203 ARG A 210 1 8 HELIX 10 AB1 GLY A 221 LYS A 234 1 14 HELIX 11 AB2 GLY A 246 THR A 252 5 7 HELIX 12 AB3 GLY A 266 GLU A 279 1 14 HELIX 13 AB4 GLY A 333 ARG A 338 1 6 HELIX 14 AB5 CYS A 345 GLY A 350 1 6 HELIX 15 AB6 PRO A 351 LYS A 354 5 4 HELIX 16 AB7 GLY A 364 VAL A 378 1 15 HELIX 17 AB8 ASP A 393 LEU A 403 1 11 HELIX 18 AB9 THR A 455 GLU A 459 5 5 HELIX 19 AC1 GLN A 496 THR A 518 1 23 SHEET 1 AA1 8 VAL A 50 GLU A 54 0 SHEET 2 AA1 8 VAL A 21 THR A 26 1 N ALA A 25 O LYS A 53 SHEET 3 AA1 8 SER A 64 THR A 68 -1 O LEU A 66 N ILE A 24 SHEET 4 AA1 8 ARG A 77 ALA A 79 -1 O PHE A 78 N PHE A 65 SHEET 5 AA1 8 ILE A 149 ASP A 155 1 O ALA A 153 N ALA A 79 SHEET 6 AA1 8 PHE A 119 TYR A 125 1 N THR A 123 O ILE A 154 SHEET 7 AA1 8 ALA A 173 VAL A 176 -1 O PHE A 175 N GLU A 122 SHEET 8 AA1 8 LYS A 179 GLN A 183 -1 O LYS A 179 N VAL A 176 SHEET 1 AA2 5 VAL A 282 ILE A 285 0 SHEET 2 AA2 5 THR A 238 MET A 241 1 N LEU A 240 O ASP A 283 SHEET 3 AA2 5 VAL A 215 VAL A 218 1 N ILE A 217 O MET A 241 SHEET 4 AA2 5 ILE A 318 VAL A 320 1 O ILE A 319 N VAL A 218 SHEET 5 AA2 5 VAL A 483 ALA A 485 1 O PHE A 484 N ILE A 318 SHEET 1 AA3 2 ASP A 254 ILE A 255 0 SHEET 2 AA3 2 THR A 264 GLU A 265 -1 O THR A 264 N ILE A 255 SHEET 1 AA4 3 ALA A 290 ILE A 294 0 SHEET 2 AA4 3 HIS A 303 THR A 307 -1 O GLU A 306 N SER A 291 SHEET 3 AA4 3 VAL A 312 ALA A 315 -1 O ALA A 315 N HIS A 303 SHEET 1 AA5 2 ALA A 324 TRP A 326 0 SHEET 2 AA5 2 LEU A 451 PRO A 453 -1 O LEU A 452 N LYS A 325 SHEET 1 AA6 5 VAL A 342 THR A 343 0 SHEET 2 AA6 5 GLY A 444 VAL A 447 1 O VAL A 447 N THR A 343 SHEET 3 AA6 5 ARG A 357 ILE A 361 1 N ALA A 359 O PHE A 446 SHEET 4 AA6 5 HIS A 380 LEU A 384 1 O THR A 382 N VAL A 360 SHEET 5 AA6 5 VAL A 406 ILE A 409 1 O ASP A 407 N LEU A 383 SHEET 1 AA7 3 ALA A 412 GLY A 419 0 SHEET 2 AA7 3 VAL A 424 ASP A 431 -1 O GLU A 428 N THR A 415 SHEET 3 AA7 3 ILE A 437 GLU A 441 -1 O HIS A 438 N TYR A 429 SSBOND 1 CYS A 129 CYS A 132 1555 1555 2.07 SSBOND 2 CYS A 345 CYS A 348 1555 1555 2.06 LINK NE2 HIS A 85 CD CD A 603 1555 1555 2.58 LINK OE1 GLU A 110 CD CD A 603 1555 4547 2.38 LINK OE2 GLU A 110 CD CD A 603 1555 4547 2.27 LINK ND1 HIS A 130 CD CD A 603 1555 1555 2.54 CISPEP 1 LYS A 62 PRO A 63 0 2.81 CISPEP 2 VAL A 171 PRO A 172 0 3.48 SITE 1 AC1 30 GLY A 219 GLY A 221 PRO A 222 ALA A 223 SITE 2 AC1 30 GLY A 242 GLU A 243 ARG A 244 GLY A 247 SITE 3 AC1 30 GLN A 248 ASN A 257 GLN A 288 ALA A 290 SITE 4 AC1 30 ALA A 321 THR A 322 GLY A 323 CYS A 348 SITE 5 AC1 30 ASN A 454 GLY A 487 ASP A 488 LYS A 495 SITE 6 AC1 30 GLN A 496 ILE A 497 ALA A 500 HOH A 707 SITE 7 AC1 30 HOH A 722 HOH A 723 HOH A 732 HOH A 737 SITE 8 AC1 30 HOH A 742 HOH A 760 SITE 1 AC2 17 ILE A 361 GLY A 362 GLY A 363 GLY A 364 SITE 2 AC2 17 ASN A 365 SER A 366 GLU A 369 LEU A 384 SITE 3 AC2 17 GLU A 385 PHE A 386 LYS A 391 ILE A 449 SITE 4 AC2 17 MET A 467 HOH A 706 HOH A 733 HOH A 745 SITE 5 AC2 17 HOH A 748 SITE 1 AC3 4 HIS A 85 GLU A 110 HIS A 114 HIS A 130 SITE 1 AC4 5 PRO A 453 ASN A 454 THR A 455 ASN A 456 SITE 2 AC4 5 TRP A 457 SITE 1 AC5 4 HIS A 438 ASN A 439 HOH A 754 HOH A 785 SITE 1 AC6 4 GLY A 333 GLU A 334 ASP A 335 GLN A 336 SITE 1 AC7 3 ASP A 393 GLN A 394 HOH A 774 SITE 1 AC8 3 ASP A 473 ALA A 474 HOH A 716 SITE 1 AC9 2 ARG A 357 HIS A 380 SITE 1 AD1 3 ILE A 440 GLU A 441 HOH A 758 SITE 1 AD2 3 ARG A 210 ASP A 211 ARG A 237 SITE 1 AD3 2 ARG A 517 HOH A 777 SITE 1 AD4 4 GLN A 413 ARG A 432 HOH A 729 HOH A 767 SITE 1 AD5 3 LYS A 340 LEU A 352 PHE A 353 SITE 1 AD6 2 SER A 30 ALA A 31 SITE 1 AD7 2 ARG A 466 PEG A 617 SITE 1 AD8 3 ASN A 465 THR A 491 GOL A 616 SITE 1 AD9 2 LYS A 354 GLY A 355 SITE 1 AE1 1 ASP A 281 CRYST1 107.090 59.390 121.350 90.00 111.34 90.00 C 1 2 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 0.009338 0.000000 0.003648 0.00000 SCALE2 0.000000 0.016838 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008847 0.00000