HEADER OXIDOREDUCTASE 20-AUG-12 4GPF TITLE STRUCTURE OF THE FE3+-BILIVERDIN-HMUO, HEME OXYGENASE FROM TITLE 2 CORYNEBACTERIUM DIPHTHERIAE (DATA SET III) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEME OXYGENASE; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 1.14.99.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM DIPHTHERIAE; SOURCE 3 ORGANISM_TAXID: 1717; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HELIX, HEME DEGRADATION, HEME, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.UNNO,M.IKEDA-SAITO REVDAT 2 20-MAR-24 4GPF 1 REMARK LINK REVDAT 1 21-AUG-13 4GPF 0 JRNL AUTH M.UNNO,A.ARDEVOL,C.ROVIRA,M.IKEDA-SAITO JRNL TITL CRYSTAL STRUCTURE OF THE SUBSTRATE-FREE AND THE JRNL TITL 2 PRODUCT-BOUND FORMS OF HMUO, A HEME OXYGENASE FROM JRNL TITL 3 CORYNEBACTERIUM DIPHTHERIAE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 49030 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5490 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3154 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE SET COUNT : 340 REMARK 3 BIN FREE R VALUE : 0.4540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4946 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 190 REMARK 3 SOLVENT ATOMS : 348 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.30000 REMARK 3 B22 (A**2) : 0.15000 REMARK 3 B33 (A**2) : -0.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.59000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.158 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.144 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5242 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7107 ; 2.046 ; 2.055 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 621 ; 5.549 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 269 ;32.580 ;23.717 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 851 ;14.895 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;14.579 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 753 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4067 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2732 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3566 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 368 ; 0.163 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 78 ; 0.208 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.136 ; 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): 3169 ; 1.067 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4903 ; 1.656 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2400 ; 2.931 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2204 ; 4.481 ; 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 : 3 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 7 A 213 REMARK 3 ORIGIN FOR THE GROUP (A): 23.5980 0.7590 -0.0970 REMARK 3 T TENSOR REMARK 3 T11: -0.0526 T22: -0.0350 REMARK 3 T33: -0.0691 T12: 0.0178 REMARK 3 T13: 0.0503 T23: -0.0081 REMARK 3 L TENSOR REMARK 3 L11: 1.5445 L22: 2.0486 REMARK 3 L33: 1.8212 L12: 0.4599 REMARK 3 L13: 0.6795 L23: 0.2577 REMARK 3 S TENSOR REMARK 3 S11: 0.0881 S12: 0.0207 S13: -0.0060 REMARK 3 S21: 0.0733 S22: -0.0736 S23: 0.0235 REMARK 3 S31: 0.0003 S32: 0.0266 S33: -0.0145 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 307 B 515 REMARK 3 ORIGIN FOR THE GROUP (A): 7.4660 16.1820 27.3020 REMARK 3 T TENSOR REMARK 3 T11: -0.0712 T22: 0.0565 REMARK 3 T33: -0.0712 T12: 0.0000 REMARK 3 T13: 0.0501 T23: 0.0136 REMARK 3 L TENSOR REMARK 3 L11: 1.9494 L22: 0.9081 REMARK 3 L33: 0.9163 L12: 0.4277 REMARK 3 L13: -0.3552 L23: 0.0146 REMARK 3 S TENSOR REMARK 3 S11: -0.0599 S12: 0.1332 S13: -0.0279 REMARK 3 S21: -0.1252 S22: 0.0802 S23: -0.0037 REMARK 3 S31: -0.0615 S32: -0.0745 S33: -0.0203 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 606 C 813 REMARK 3 ORIGIN FOR THE GROUP (A): 29.0960 6.0800 51.3950 REMARK 3 T TENSOR REMARK 3 T11: -0.0925 T22: 0.0831 REMARK 3 T33: -0.0347 T12: 0.0057 REMARK 3 T13: 0.0397 T23: 0.0492 REMARK 3 L TENSOR REMARK 3 L11: 1.7574 L22: 0.6965 REMARK 3 L33: 1.0563 L12: -0.3362 REMARK 3 L13: -0.4136 L23: -0.4034 REMARK 3 S TENSOR REMARK 3 S11: -0.0784 S12: -0.2193 S13: -0.0402 REMARK 3 S21: 0.0888 S22: -0.0539 S23: -0.0993 REMARK 3 S31: -0.0063 S32: 0.1250 S33: 0.1323 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 3 POSITIONS REMARK 4 REMARK 4 4GPF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074472. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54735 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.1 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 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MES, PH 6.1, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 303K 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 31.26950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 350 REMARK 350 BIOMOLECULE: 3 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: C 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 MET A 1 REMARK 465 THR A 2 REMARK 465 THR A 3 REMARK 465 ALA A 4 REMARK 465 THR A 5 REMARK 465 ALA A 6 REMARK 465 GLY A 214 REMARK 465 LEU A 215 REMARK 465 MET B 301 REMARK 465 THR B 302 REMARK 465 THR B 303 REMARK 465 ALA B 304 REMARK 465 THR B 305 REMARK 465 ALA B 306 REMARK 465 MET C 601 REMARK 465 THR C 602 REMARK 465 THR C 603 REMARK 465 ALA C 604 REMARK 465 THR C 605 REMARK 465 GLY C 814 REMARK 465 LEU C 815 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 LYS A 22 CG CD CE NZ REMARK 470 LYS A 195 CG CD CE NZ REMARK 470 GLU B 321 CG CD OE1 OE2 REMARK 470 GLN B 441 CG CD OE1 NE2 REMARK 470 LYS C 689 CG CD CE NZ REMARK 470 GLU C 756 CG CD OE1 OE2 REMARK 470 LYS C 813 CG CD CE 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 OE2 GLU C 647 NH1 ARG C 699 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 112 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP C 754 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 GLY C 765 N - CA - C ANGL. DEV. = -18.5 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 LEU A 37 -127.59 -111.89 REMARK 500 LEU A 73 57.14 -91.24 REMARK 500 SER A 93 -173.82 -174.20 REMARK 500 ALA A 167 -84.91 -86.52 REMARK 500 LEU B 337 -130.58 -102.99 REMARK 500 SER B 438 -94.87 -98.20 REMARK 500 LEU C 637 -133.08 -101.81 REMARK 500 PHE C 763 -70.90 -107.96 REMARK 500 GLU C 764 75.40 26.45 REMARK 500 ILE C 766 105.42 -59.92 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 GLU C 764 GLY C 765 124.30 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 FE A 902 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 20 NE2 REMARK 620 2 BLA A 901 NA 86.5 REMARK 620 3 BLA A 901 NB 74.1 92.7 REMARK 620 4 BLA A 901 NC 119.5 152.6 102.3 REMARK 620 5 BLA A 901 ND 93.6 88.1 167.7 82.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BLA A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BLA B 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BLA C 905 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IW0 RELATED DB: PDB REMARK 900 RELATED ID: 1IW1 RELATED DB: PDB REMARK 900 RELATED ID: 4GOH RELATED DB: PDB REMARK 900 RELATED ID: 4GPC RELATED DB: PDB REMARK 900 RELATED ID: 4GPH RELATED DB: PDB DBREF 4GPF A 1 215 UNP Q54AI1 Q54AI1_CORDP 1 215 DBREF 4GPF B 301 515 UNP Q54AI1 Q54AI1_CORDP 1 215 DBREF 4GPF C 601 815 UNP Q54AI1 Q54AI1_CORDP 1 215 SEQRES 1 A 215 MET THR THR ALA THR ALA GLY LEU ALA VAL GLU LEU LYS SEQRES 2 A 215 GLN SER THR ALA GLN ALA HIS GLU LYS ALA GLU HIS SER SEQRES 3 A 215 THR PHE MET SER ASP LEU LEU LYS GLY ARG LEU GLY VAL SEQRES 4 A 215 ALA GLU PHE THR ARG LEU GLN GLU GLN ALA TRP LEU PHE SEQRES 5 A 215 TYR THR ALA LEU GLU GLN ALA VAL ASP ALA VAL ARG ALA SEQRES 6 A 215 SER GLY PHE ALA GLU SER LEU LEU ASP PRO ALA LEU ASN SEQRES 7 A 215 ARG ALA GLU VAL LEU ALA ARG ASP LEU ASP LYS LEU ASN SEQRES 8 A 215 GLY SER SER GLU TRP ARG SER ARG ILE THR ALA SER PRO SEQRES 9 A 215 ALA VAL ILE ASP TYR VAL ASN ARG LEU GLU GLU ILE ARG SEQRES 10 A 215 ASP ASN VAL ASP GLY PRO ALA LEU VAL ALA HIS HIS TYR SEQRES 11 A 215 VAL ARG TYR LEU GLY ASP LEU SER GLY GLY GLN VAL ILE SEQRES 12 A 215 ALA ARG MET MET GLN ARG HIS TYR GLY VAL ASP PRO GLU SEQRES 13 A 215 ALA LEU GLY PHE TYR HIS PHE GLU GLY ILE ALA LYS LEU SEQRES 14 A 215 LYS VAL TYR LYS ASP GLU TYR ARG GLU LYS LEU ASN ASN SEQRES 15 A 215 LEU GLU LEU SER ASP GLU GLN ARG GLU HIS LEU LEU LYS SEQRES 16 A 215 GLU ALA THR ASP ALA PHE VAL PHE ASN HIS GLN VAL PHE SEQRES 17 A 215 ALA ASP LEU GLY LYS GLY LEU SEQRES 1 B 215 MET THR THR ALA THR ALA GLY LEU ALA VAL GLU LEU LYS SEQRES 2 B 215 GLN SER THR ALA GLN ALA HIS GLU LYS ALA GLU HIS SER SEQRES 3 B 215 THR PHE MET SER ASP LEU LEU LYS GLY ARG LEU GLY VAL SEQRES 4 B 215 ALA GLU PHE THR ARG LEU GLN GLU GLN ALA TRP LEU PHE SEQRES 5 B 215 TYR THR ALA LEU GLU GLN ALA VAL ASP ALA VAL ARG ALA SEQRES 6 B 215 SER GLY PHE ALA GLU SER LEU LEU ASP PRO ALA LEU ASN SEQRES 7 B 215 ARG ALA GLU VAL LEU ALA ARG ASP LEU ASP LYS LEU ASN SEQRES 8 B 215 GLY SER SER GLU TRP ARG SER ARG ILE THR ALA SER PRO SEQRES 9 B 215 ALA VAL ILE ASP TYR VAL ASN ARG LEU GLU GLU ILE ARG SEQRES 10 B 215 ASP ASN VAL ASP GLY PRO ALA LEU VAL ALA HIS HIS TYR SEQRES 11 B 215 VAL ARG TYR LEU GLY ASP LEU SER GLY GLY GLN VAL ILE SEQRES 12 B 215 ALA ARG MET MET GLN ARG HIS TYR GLY VAL ASP PRO GLU SEQRES 13 B 215 ALA LEU GLY PHE TYR HIS PHE GLU GLY ILE ALA LYS LEU SEQRES 14 B 215 LYS VAL TYR LYS ASP GLU TYR ARG GLU LYS LEU ASN ASN SEQRES 15 B 215 LEU GLU LEU SER ASP GLU GLN ARG GLU HIS LEU LEU LYS SEQRES 16 B 215 GLU ALA THR ASP ALA PHE VAL PHE ASN HIS GLN VAL PHE SEQRES 17 B 215 ALA ASP LEU GLY LYS GLY LEU SEQRES 1 C 215 MET THR THR ALA THR ALA GLY LEU ALA VAL GLU LEU LYS SEQRES 2 C 215 GLN SER THR ALA GLN ALA HIS GLU LYS ALA GLU HIS SER SEQRES 3 C 215 THR PHE MET SER ASP LEU LEU LYS GLY ARG LEU GLY VAL SEQRES 4 C 215 ALA GLU PHE THR ARG LEU GLN GLU GLN ALA TRP LEU PHE SEQRES 5 C 215 TYR THR ALA LEU GLU GLN ALA VAL ASP ALA VAL ARG ALA SEQRES 6 C 215 SER GLY PHE ALA GLU SER LEU LEU ASP PRO ALA LEU ASN SEQRES 7 C 215 ARG ALA GLU VAL LEU ALA ARG ASP LEU ASP LYS LEU ASN SEQRES 8 C 215 GLY SER SER GLU TRP ARG SER ARG ILE THR ALA SER PRO SEQRES 9 C 215 ALA VAL ILE ASP TYR VAL ASN ARG LEU GLU GLU ILE ARG SEQRES 10 C 215 ASP ASN VAL ASP GLY PRO ALA LEU VAL ALA HIS HIS TYR SEQRES 11 C 215 VAL ARG TYR LEU GLY ASP LEU SER GLY GLY GLN VAL ILE SEQRES 12 C 215 ALA ARG MET MET GLN ARG HIS TYR GLY VAL ASP PRO GLU SEQRES 13 C 215 ALA LEU GLY PHE TYR HIS PHE GLU GLY ILE ALA LYS LEU SEQRES 14 C 215 LYS VAL TYR LYS ASP GLU TYR ARG GLU LYS LEU ASN ASN SEQRES 15 C 215 LEU GLU LEU SER ASP GLU GLN ARG GLU HIS LEU LEU LYS SEQRES 16 C 215 GLU ALA THR ASP ALA PHE VAL PHE ASN HIS GLN VAL PHE SEQRES 17 C 215 ALA ASP LEU GLY LYS GLY LEU HET BLA A 901 43 HET FE A 902 1 HET SO4 A 903 5 HET SO4 A 904 5 HET SO4 A 905 5 HET SO4 B 601 5 HET SO4 B 602 5 HET SO4 B 603 5 HET SO4 B 604 5 HET SO4 B 605 5 HET BLA B 606 43 HET SO4 C 901 5 HET SO4 C 902 5 HET SO4 C 903 5 HET SO4 C 904 5 HET BLA C 905 43 HETNAM BLA BILIVERDINE IX ALPHA HETNAM FE FE (III) ION HETNAM SO4 SULFATE ION FORMUL 4 BLA 3(C33 H34 N4 O6) FORMUL 5 FE FE 3+ FORMUL 6 SO4 12(O4 S 2-) FORMUL 20 HOH *348(H2 O) HELIX 1 1 GLY A 7 HIS A 25 1 19 HELIX 2 2 SER A 26 LYS A 34 1 9 HELIX 3 3 GLY A 38 SER A 66 1 29 HELIX 4 4 ALA A 69 LEU A 73 5 5 HELIX 5 5 ASP A 74 ASN A 78 5 5 HELIX 6 6 ARG A 79 GLY A 92 1 14 HELIX 7 7 GLU A 95 ILE A 100 1 6 HELIX 8 8 SER A 103 VAL A 120 1 18 HELIX 9 9 ASP A 121 GLY A 152 1 32 HELIX 10 10 ASP A 154 HIS A 162 5 9 HELIX 11 11 LYS A 168 LEU A 183 1 16 HELIX 12 12 SER A 186 LYS A 213 1 28 HELIX 13 13 LEU B 308 THR B 316 1 9 HELIX 14 14 THR B 316 HIS B 325 1 10 HELIX 15 15 SER B 326 LYS B 334 1 9 HELIX 16 16 GLY B 338 SER B 366 1 29 HELIX 17 17 ASP B 374 ASN B 378 5 5 HELIX 18 18 ARG B 379 GLY B 392 1 14 HELIX 19 19 SER B 394 ARG B 399 5 6 HELIX 20 20 SER B 403 VAL B 420 1 18 HELIX 21 21 ASP B 421 SER B 438 1 18 HELIX 22 22 GLY B 439 GLY B 452 1 14 HELIX 23 23 ASP B 454 HIS B 462 5 9 HELIX 24 24 LYS B 468 LEU B 483 1 16 HELIX 25 25 SER B 486 GLY B 514 1 29 HELIX 26 26 GLY C 607 THR C 616 1 10 HELIX 27 27 THR C 616 HIS C 625 1 10 HELIX 28 28 SER C 626 LYS C 634 1 9 HELIX 29 29 GLY C 638 SER C 666 1 29 HELIX 30 30 ASP C 674 ASN C 678 5 5 HELIX 31 31 ARG C 679 GLY C 692 1 14 HELIX 32 32 SER C 694 ARG C 699 5 6 HELIX 33 33 SER C 703 VAL C 720 1 18 HELIX 34 34 ASP C 721 GLY C 752 1 32 HELIX 35 35 ASP C 754 HIS C 762 5 9 HELIX 36 36 LYS C 768 LEU C 783 1 16 HELIX 37 37 SER C 786 GLY C 812 1 27 LINK NE2 HIS A 20 FE FE A 902 1555 1555 2.09 LINK NA BLA A 901 FE FE A 902 1555 1555 2.05 LINK NB BLA A 901 FE FE A 902 1555 1555 2.07 LINK NC BLA A 901 FE FE A 902 1555 1555 2.23 LINK ND BLA A 901 FE FE A 902 1555 1555 2.25 SITE 1 AC1 19 LYS A 13 HIS A 20 GLU A 24 MET A 29 SITE 2 AC1 19 LEU A 33 TYR A 130 VAL A 131 GLY A 135 SITE 3 AC1 19 SER A 138 ARG A 177 PHE A 201 ASN A 204 SITE 4 AC1 19 PHE A 208 FE A 902 SO4 A 905 HOH A1039 SITE 5 AC1 19 HOH A1062 HOH A1069 HOH A1070 SITE 1 AC2 2 HIS A 20 BLA A 901 SITE 1 AC3 6 GLY A 67 ALA A 69 GLU A 70 SER A 71 SITE 2 AC3 6 HOH A1021 HOH A1036 SITE 1 AC4 4 SER A 26 THR A 27 HIS A 205 HOH A1038 SITE 1 AC5 3 LYS A 173 ARG A 177 BLA A 901 SITE 1 AC6 4 SER B 326 THR B 327 HIS B 505 HOH B 785 SITE 1 AC7 4 LYS B 470 LYS B 473 ARG B 477 HOH B 792 SITE 1 AC8 7 GLY B 367 ALA B 369 GLU B 370 SER B 371 SITE 2 AC8 7 HOH B 747 HOH B 761 HOH B 787 SITE 1 AC9 2 ARG B 385 HOH B 706 SITE 1 BC1 1 ARG B 399 SITE 1 BC2 16 LYS B 313 HIS B 320 GLU B 324 MET B 329 SITE 2 BC2 16 LEU B 333 TYR B 430 VAL B 431 GLY B 435 SITE 3 BC2 16 SER B 438 GLY B 439 ILE B 443 ARG B 477 SITE 4 BC2 16 PHE B 501 PHE B 508 HOH B 726 HOH B 814 SITE 1 BC3 4 SER C 626 THR C 627 HIS C 805 HOH C1129 SITE 1 BC4 3 GLY C 638 VAL C 639 ALA C 640 SITE 1 BC5 6 ALA C 669 GLU C 670 SER C 671 HOH C1021 SITE 2 BC5 6 HOH C1069 HOH C1075 SITE 1 BC6 4 VAL C 682 ARG C 685 HOH C1018 HOH C1026 SITE 1 BC7 17 LYS C 613 HIS C 620 ALA C 623 GLU C 624 SITE 2 BC7 17 TYR C 730 VAL C 731 GLY C 735 SER C 738 SITE 3 BC7 17 ILE C 743 ARG C 777 PHE C 808 HOH C1023 SITE 4 BC7 17 HOH C1029 HOH C1057 HOH C1066 HOH C1105 SITE 5 BC7 17 HOH C1106 CRYST1 53.937 62.539 107.589 90.00 101.09 90.00 P 1 21 1 6 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 0.018540 0.000000 0.003635 0.00000 SCALE2 0.000000 0.015990 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009472 0.00000