HEADER OXIDOREDUCTASE 05-JAN-11 2Y4F TITLE X-RAY CRYSTALLOGRAPHIC STRUCTURE OF E. COLI HEME-EFEB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXIDASE YCDB; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: EFEB; COMPND 5 EC: 1.11.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PEHISTEV KEYWDS IRON UPTAKE, OXIDOREDUCTASE, DYP-PEROXIDASE-LIKE, DEFERROCHELATASE EXPDTA X-RAY DIFFRACTION AUTHOR V.A.BAMFORD,S.C.ANDREWS,K.A.WATSON REVDAT 3 20-DEC-23 2Y4F 1 REMARK SHEET REVDAT 2 22-MAY-19 2Y4F 1 REMARK REVDAT 1 26-JAN-11 2Y4F 0 JRNL AUTH V.A.BAMFORD,S.C.ANDREWS,K.A.WATSON JRNL TITL EFEB, THE PEROXIDASE COMPONENT OF THE EFEUOB BACTERIAL JRNL TITL 2 FE(II) TRANSPORT SYSTEM, ALSO SHOWS NOVEL REMOVAL OF IRON JRNL TITL 3 FROM HEME JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 22545 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1209 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1634 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.4010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5996 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 142 REMARK 3 SOLVENT ATOMS : 202 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.81000 REMARK 3 B22 (A**2) : 2.14000 REMARK 3 B33 (A**2) : 0.67000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.418 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.300 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.684 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.858 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6279 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8547 ; 1.310 ; 2.019 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 766 ; 6.172 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 288 ;37.532 ;24.167 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1026 ;17.656 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;19.298 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 906 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4822 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3824 ; 0.502 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6142 ; 0.953 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2455 ; 1.265 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2405 ; 2.132 ; 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 : 1.40 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. REMARK 4 REMARK 4 2Y4F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1290046117. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23867 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 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: PDB ENTRY 2Y4D REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE, 5% (V/V) PEG REMARK 280 400, 0.1M HEPES PH 7.0, 291K 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 41.66500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.96500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.66500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.96500 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: 9030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -164.6 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 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 -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 ALA A 0 REMARK 465 GLN A 1 REMARK 465 LYS A 2 REMARK 465 THR A 3 REMARK 465 GLN A 4 REMARK 465 GLY B -3 REMARK 465 ALA B -2 REMARK 465 MET B -1 REMARK 465 ALA B 0 REMARK 465 GLN B 1 REMARK 465 LYS B 2 REMARK 465 THR B 3 REMARK 465 GLN B 4 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 O1 SO4 A 400 O HOH A 2105 2.02 REMARK 500 NE ARG B 175 O HOH B 2044 2.15 REMARK 500 OD1 ASP A 43 O HOH A 2013 2.16 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 ILE A 29 -60.67 -102.31 REMARK 500 PRO A 32 157.44 -46.37 REMARK 500 ASP A 109 -156.82 -86.39 REMARK 500 HIS A 139 -161.62 69.94 REMARK 500 ARG A 172 -87.83 -84.68 REMARK 500 THR A 202 -56.60 -29.22 REMARK 500 ASN A 209 86.77 -69.21 REMARK 500 ASP A 210 -68.39 -27.00 REMARK 500 ARG A 301 75.24 37.69 REMARK 500 THR A 302 -159.88 -132.78 REMARK 500 GLU A 306 -43.62 -18.16 REMARK 500 LEU A 319 -108.26 -109.10 REMARK 500 LEU A 371 152.91 -48.97 REMARK 500 ASP A 376 -166.47 -176.85 REMARK 500 ILE B 29 -70.21 -133.92 REMARK 500 PHE B 108 40.36 -105.38 REMARK 500 HIS B 139 -147.85 68.62 REMARK 500 ARG B 172 -61.14 -106.33 REMARK 500 SER B 186 4.38 -59.94 REMARK 500 LYS B 187 49.71 38.63 REMARK 500 ASP B 222 3.40 -68.51 REMARK 500 GLN B 224 -1.22 -59.98 REMARK 500 VAL B 288 -62.98 -97.57 REMARK 500 ALA B 303 -21.36 65.65 REMARK 500 LEU B 319 -110.47 -108.31 REMARK 500 ASN B 352 109.79 -48.24 REMARK 500 ARG B 387 -91.56 -90.83 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 389 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 294 NE2 REMARK 620 2 HEM A 389 NA 94.9 REMARK 620 3 HEM A 389 NB 93.1 86.7 REMARK 620 4 HEM A 389 NC 85.9 178.2 91.7 REMARK 620 5 HEM A 389 ND 88.1 94.6 178.2 87.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 389 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 294 NE2 REMARK 620 2 HEM B 389 NA 94.1 REMARK 620 3 HEM B 389 NB 91.8 91.5 REMARK 620 4 HEM B 389 NC 89.7 176.0 89.4 REMARK 620 5 HEM B 389 ND 91.1 90.3 176.4 88.5 REMARK 620 N 1 2 3 4 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. 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 389 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 389 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Y4E RELATED DB: PDB REMARK 900 X-RAY CRYSTALLOGRAPHIC STRUCTURE OF E. COLI PPIX-EFEB REMARK 900 RELATED ID: 2Y4D RELATED DB: PDB REMARK 900 X-RAY CRYSTALLOGRAPHIC STRUCTURE OF E. COLI APO-EFEB DBREF 2Y4F A 1 388 UNP P31545 YCDB_ECOLI 36 423 DBREF 2Y4F B 1 388 UNP P31545 YCDB_ECOLI 36 423 SEQADV 2Y4F GLY A -3 UNP P31545 EXPRESSION TAG SEQADV 2Y4F ALA A -2 UNP P31545 EXPRESSION TAG SEQADV 2Y4F MET A -1 UNP P31545 EXPRESSION TAG SEQADV 2Y4F ALA A 0 UNP P31545 EXPRESSION TAG SEQADV 2Y4F GLY B -3 UNP P31545 EXPRESSION TAG SEQADV 2Y4F ALA B -2 UNP P31545 EXPRESSION TAG SEQADV 2Y4F MET B -1 UNP P31545 EXPRESSION TAG SEQADV 2Y4F ALA B 0 UNP P31545 EXPRESSION TAG SEQRES 1 A 392 GLY ALA MET ALA GLN LYS THR GLN SER ALA PRO GLY THR SEQRES 2 A 392 LEU SER PRO ASP ALA ARG ASN GLU LYS GLN PRO PHE TYR SEQRES 3 A 392 GLY GLU HIS GLN ALA GLY ILE LEU THR PRO GLN GLN ALA SEQRES 4 A 392 ALA MET MET LEU VAL ALA PHE ASP VAL LEU ALA SER ASP SEQRES 5 A 392 LYS ALA ASP LEU GLU ARG LEU PHE ARG LEU LEU THR GLN SEQRES 6 A 392 ARG PHE ALA PHE LEU THR GLN GLY GLY ALA ALA PRO GLU SEQRES 7 A 392 THR PRO ASN PRO ARG LEU PRO PRO LEU ASP SER GLY ILE SEQRES 8 A 392 LEU GLY GLY TYR ILE ALA PRO ASP ASN LEU THR ILE THR SEQRES 9 A 392 LEU SER VAL GLY HIS SER LEU PHE ASP GLU ARG PHE GLY SEQRES 10 A 392 LEU ALA PRO GLN MET PRO LYS LYS LEU GLN LYS MET THR SEQRES 11 A 392 ARG PHE PRO ASN ASP SER LEU ASP ALA ALA LEU CYS HIS SEQRES 12 A 392 GLY ASP VAL LEU LEU GLN ILE CYS ALA ASN THR GLN ASP SEQRES 13 A 392 THR VAL ILE HIS ALA LEU ARG ASP ILE ILE LYS HIS THR SEQRES 14 A 392 PRO ASP LEU LEU SER VAL ARG TRP LYS ARG GLU GLY PHE SEQRES 15 A 392 ILE SER ASP HIS ALA ALA ARG SER LYS GLY LYS GLU THR SEQRES 16 A 392 PRO ILE ASN LEU LEU GLY PHE LYS ASP GLY THR ALA ASN SEQRES 17 A 392 PRO ASP SER GLN ASN ASP LYS LEU MET GLN LYS VAL VAL SEQRES 18 A 392 TRP VAL THR ALA ASP GLN GLN GLU PRO ALA TRP THR ILE SEQRES 19 A 392 GLY GLY SER TYR GLN ALA VAL ARG LEU ILE GLN PHE ARG SEQRES 20 A 392 VAL GLU PHE TRP ASP ARG THR PRO LEU LYS GLU GLN GLN SEQRES 21 A 392 THR ILE PHE GLY ARG ASP LYS GLN THR GLY ALA PRO LEU SEQRES 22 A 392 GLY MET GLN HIS GLU HIS ASP VAL PRO ASP TYR ALA SER SEQRES 23 A 392 ASP PRO GLU GLY LYS VAL ILE ALA LEU ASP SER HIS ILE SEQRES 24 A 392 ARG LEU ALA ASN PRO ARG THR ALA GLU SER GLU SER SER SEQRES 25 A 392 LEU MET LEU ARG ARG GLY TYR SER TYR SER LEU GLY VAL SEQRES 26 A 392 THR ASN SER GLY GLN LEU ASP MET GLY LEU LEU PHE VAL SEQRES 27 A 392 CYS TYR GLN HIS ASP LEU GLU LYS GLY PHE LEU THR VAL SEQRES 28 A 392 GLN LYS ARG LEU ASN GLY GLU ALA LEU GLU GLU TYR VAL SEQRES 29 A 392 LYS PRO ILE GLY GLY GLY TYR PHE PHE ALA LEU PRO GLY SEQRES 30 A 392 VAL LYS ASP ALA ASN ASP TYR PHE GLY SER ALA LEU LEU SEQRES 31 A 392 ARG VAL SEQRES 1 B 392 GLY ALA MET ALA GLN LYS THR GLN SER ALA PRO GLY THR SEQRES 2 B 392 LEU SER PRO ASP ALA ARG ASN GLU LYS GLN PRO PHE TYR SEQRES 3 B 392 GLY GLU HIS GLN ALA GLY ILE LEU THR PRO GLN GLN ALA SEQRES 4 B 392 ALA MET MET LEU VAL ALA PHE ASP VAL LEU ALA SER ASP SEQRES 5 B 392 LYS ALA ASP LEU GLU ARG LEU PHE ARG LEU LEU THR GLN SEQRES 6 B 392 ARG PHE ALA PHE LEU THR GLN GLY GLY ALA ALA PRO GLU SEQRES 7 B 392 THR PRO ASN PRO ARG LEU PRO PRO LEU ASP SER GLY ILE SEQRES 8 B 392 LEU GLY GLY TYR ILE ALA PRO ASP ASN LEU THR ILE THR SEQRES 9 B 392 LEU SER VAL GLY HIS SER LEU PHE ASP GLU ARG PHE GLY SEQRES 10 B 392 LEU ALA PRO GLN MET PRO LYS LYS LEU GLN LYS MET THR SEQRES 11 B 392 ARG PHE PRO ASN ASP SER LEU ASP ALA ALA LEU CYS HIS SEQRES 12 B 392 GLY ASP VAL LEU LEU GLN ILE CYS ALA ASN THR GLN ASP SEQRES 13 B 392 THR VAL ILE HIS ALA LEU ARG ASP ILE ILE LYS HIS THR SEQRES 14 B 392 PRO ASP LEU LEU SER VAL ARG TRP LYS ARG GLU GLY PHE SEQRES 15 B 392 ILE SER ASP HIS ALA ALA ARG SER LYS GLY LYS GLU THR SEQRES 16 B 392 PRO ILE ASN LEU LEU GLY PHE LYS ASP GLY THR ALA ASN SEQRES 17 B 392 PRO ASP SER GLN ASN ASP LYS LEU MET GLN LYS VAL VAL SEQRES 18 B 392 TRP VAL THR ALA ASP GLN GLN GLU PRO ALA TRP THR ILE SEQRES 19 B 392 GLY GLY SER TYR GLN ALA VAL ARG LEU ILE GLN PHE ARG SEQRES 20 B 392 VAL GLU PHE TRP ASP ARG THR PRO LEU LYS GLU GLN GLN SEQRES 21 B 392 THR ILE PHE GLY ARG ASP LYS GLN THR GLY ALA PRO LEU SEQRES 22 B 392 GLY MET GLN HIS GLU HIS ASP VAL PRO ASP TYR ALA SER SEQRES 23 B 392 ASP PRO GLU GLY LYS VAL ILE ALA LEU ASP SER HIS ILE SEQRES 24 B 392 ARG LEU ALA ASN PRO ARG THR ALA GLU SER GLU SER SER SEQRES 25 B 392 LEU MET LEU ARG ARG GLY TYR SER TYR SER LEU GLY VAL SEQRES 26 B 392 THR ASN SER GLY GLN LEU ASP MET GLY LEU LEU PHE VAL SEQRES 27 B 392 CYS TYR GLN HIS ASP LEU GLU LYS GLY PHE LEU THR VAL SEQRES 28 B 392 GLN LYS ARG LEU ASN GLY GLU ALA LEU GLU GLU TYR VAL SEQRES 29 B 392 LYS PRO ILE GLY GLY GLY TYR PHE PHE ALA LEU PRO GLY SEQRES 30 B 392 VAL LYS ASP ALA ASN ASP TYR PHE GLY SER ALA LEU LEU SEQRES 31 B 392 ARG VAL HET HEM A 389 43 HET SO4 A 400 5 HET SO4 A 401 5 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET SO4 A 406 5 HET GOL A 407 6 HET HEM B 389 43 HET SO4 B 400 5 HET SO4 B 401 5 HET SO4 B 402 5 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN HEM HEME HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 SO4 10(O4 S 2-) FORMUL 11 GOL C3 H8 O3 FORMUL 16 HOH *202(H2 O) HELIX 1 1 ASP A 48 GLY A 69 1 22 HELIX 2 2 SER A 106 ASP A 109 5 4 HELIX 3 3 LEU A 114 MET A 118 5 5 HELIX 4 4 ASP A 134 LEU A 137 5 4 HELIX 5 5 THR A 150 HIS A 164 1 15 HELIX 6 6 SER A 180 SER A 186 1 7 HELIX 7 7 ASN A 209 VAL A 217 1 9 HELIX 8 8 PRO A 226 ILE A 230 5 5 HELIX 9 9 ARG A 243 ARG A 249 1 7 HELIX 10 10 PRO A 251 GLY A 260 1 10 HELIX 11 11 SER A 293 ASN A 299 1 7 HELIX 12 12 GLU A 304 LEU A 309 5 6 HELIX 13 13 GLY A 343 ASN A 352 1 10 HELIX 14 14 GLU A 354 GLU A 358 5 5 HELIX 15 15 GLY A 382 VAL A 388 1 7 HELIX 16 16 ASP B 48 GLY B 69 1 22 HELIX 17 17 SER B 106 ASP B 109 5 4 HELIX 18 18 LEU B 114 MET B 118 5 5 HELIX 19 19 ASP B 134 LEU B 137 5 4 HELIX 20 20 THR B 150 THR B 165 1 16 HELIX 21 21 SER B 180 SER B 186 1 7 HELIX 22 22 ASN B 209 VAL B 217 1 9 HELIX 23 23 ARG B 243 ARG B 249 1 7 HELIX 24 24 PRO B 251 GLY B 260 1 10 HELIX 25 25 ASP B 279 ASP B 283 5 5 HELIX 26 26 SER B 293 ASN B 299 1 7 HELIX 27 27 SER B 305 LEU B 309 5 5 HELIX 28 28 GLY B 343 ASN B 352 1 10 HELIX 29 29 GLU B 354 GLU B 358 5 5 HELIX 30 30 GLY B 382 ARG B 387 1 6 SHEET 1 AA 9 ALA A 36 VAL A 44 0 SHEET 2 AA 9 VAL A 142 ALA A 148 -1 O VAL A 142 N PHE A 42 SHEET 3 AA 9 THR A 98 GLY A 104 -1 O THR A 98 N CYS A 147 SHEET 4 AA 9 VAL A 360 ALA A 370 -1 O PHE A 369 N VAL A 103 SHEET 5 AA 9 SER A 233 PHE A 242 -1 O SER A 233 N ALA A 370 SHEET 6 AA 9 LEU A 327 GLN A 337 -1 O MET A 329 N PHE A 242 SHEET 7 AA 9 TYR A 315 VAL A 321 -1 O TYR A 315 N LEU A 332 SHEET 8 AA 9 LEU A 169 PHE A 178 -1 O PHE A 178 N SER A 316 SHEET 9 AA 9 ALA A 36 VAL A 44 0 SHEET 1 AB 2 GLY A 70 ALA A 71 0 SHEET 2 AB 2 TYR A 91 ILE A 92 -1 O ILE A 92 N GLY A 70 SHEET 1 BA 9 ALA B 36 VAL B 44 0 SHEET 2 BA 9 VAL B 142 ALA B 148 -1 O VAL B 142 N PHE B 42 SHEET 3 BA 9 THR B 98 GLY B 104 -1 O THR B 98 N CYS B 147 SHEET 4 BA 9 VAL B 360 ALA B 370 -1 O PHE B 369 N VAL B 103 SHEET 5 BA 9 SER B 233 PHE B 242 -1 O SER B 233 N ALA B 370 SHEET 6 BA 9 LEU B 327 GLN B 337 -1 O MET B 329 N PHE B 242 SHEET 7 BA 9 TYR B 315 VAL B 321 -1 O TYR B 315 N LEU B 332 SHEET 8 BA 9 LEU B 169 PHE B 178 -1 O PHE B 178 N SER B 316 SHEET 9 BA 9 ALA B 36 VAL B 44 0 SHEET 1 BB 2 GLY B 70 ALA B 71 0 SHEET 2 BB 2 TYR B 91 ILE B 92 -1 O ILE B 92 N GLY B 70 LINK NE2 HIS A 294 FE HEM A 389 1555 1555 2.22 LINK NE2 HIS B 294 FE HEM B 389 1555 1555 2.05 CISPEP 1 ALA A 6 PRO A 7 0 2.60 CISPEP 2 ALA B 6 PRO B 7 0 1.46 SITE 1 AC1 24 ASN A 194 LEU A 196 LYS A 199 ASP A 200 SITE 2 AC1 24 GLY A 201 THR A 202 ALA A 203 ILE A 240 SITE 3 AC1 24 PHE A 242 PHE A 259 HIS A 294 ILE A 295 SITE 4 AC1 24 ASN A 299 ARG A 301 MET A 310 ARG A 312 SITE 5 AC1 24 LEU A 331 PHE A 333 PHE A 344 GLN A 348 SITE 6 AC1 24 LEU A 351 HOH A2076 HOH A2103 HOH A2104 SITE 1 AC2 7 LEU A 137 ARG A 175 HOH A2049 HOH A2050 SITE 2 AC2 7 HOH A2105 GLY B 320 VAL B 321 SITE 1 AC3 2 ARG A 243 LYS A 361 SITE 1 AC4 3 GLN A 241 THR A 322 ASN A 323 SITE 1 AC5 5 ARG A 15 ASN A 16 THR A 126 ARG A 127 SITE 2 AC5 5 HOH A2106 SITE 1 AC6 1 ARG A 172 SITE 1 AC7 3 LYS A 120 HOH A2107 ASP B 222 SITE 1 AC8 3 HIS A 105 SER A 106 LYS A 124 SITE 1 AC9 3 ALA A 136 HOH A2109 ASN B 323 SITE 1 BC1 17 ASN B 194 LYS B 199 ASP B 200 GLY B 201 SITE 2 BC1 17 THR B 202 ALA B 203 PHE B 259 HIS B 294 SITE 3 BC1 17 ILE B 295 ASN B 299 ARG B 301 ARG B 312 SITE 4 BC1 17 PHE B 333 VAL B 347 GLN B 348 LEU B 351 SITE 5 BC1 17 HOH B2090 SITE 1 BC2 6 GLY A 320 VAL A 321 HOH A2092 LEU B 137 SITE 2 BC2 6 ARG B 175 HOH B2042 SITE 1 BC3 2 ARG B 172 HOH B2091 SITE 1 BC4 4 ARG B 243 LYS B 361 HOH B2092 HOH B2093 CRYST1 83.330 85.930 120.000 90.00 90.00 90.00 P 21 21 21 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 0.012000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011637 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008333 0.00000