HEADER OXIDOREDUCTASE 13-AUG-03 1OLT TITLE COPROPORPHYRINOGEN III OXIDASE (HEMN) FROM ESCHERICHIA COLI IS A TITLE 2 RADICAL SAM ENZYME. COMPND MOL_ID: 1; COMPND 2 MOLECULE: OXYGEN-INDEPENDENT COPROPORPHYRINOGEN III OXIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COPROPORPHYRINOGENASE, COPROGEN OXIDASE; COMPND 5 EC: 1.3.-.- SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12 KEYWDS HEME BIOSYNTHESIS, DECARBOXYLASE, RADICAL SAM ENZYME, 4FE- 4S KEYWDS 2 CLUSTER, S-ADENOSYL-L-METHIONINE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR G.LAYER,J.MOSER,D.W.HEINZ,D.JAHN,W.-D.SCHUBERT REVDAT 5 08-MAY-19 1OLT 1 REMARK REVDAT 4 13-JUL-11 1OLT 1 VERSN REVDAT 3 24-FEB-09 1OLT 1 VERSN REVDAT 2 04-JUN-04 1OLT 1 HETATM REVDAT 1 04-DEC-03 1OLT 0 JRNL AUTH G.LAYER,J.MOSER,D.W.HEINZ,D.JAHN,W.-D.SCHUBERT JRNL TITL CRYSTAL STRUCTURE OF COPROPORPHYRINOGEN III OXIDASE REVEALS JRNL TITL 2 COFACTOR GEOMETRY OF RADICAL SAM ENZYMES JRNL REF EMBO J. V. 22 6214 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 14633981 JRNL DOI 10.1093/EMBOJ/CDG598 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 32527 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) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1735 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) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2334 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1580 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.2150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3524 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 396 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.75000 REMARK 3 B22 (A**2) : 0.75000 REMARK 3 B33 (A**2) : -1.13000 REMARK 3 B12 (A**2) : 0.38000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.182 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.246 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4274 ; 0.036 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3778 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5851 ; 2.109 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8843 ; 1.019 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 539 ; 6.404 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 610 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4986 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 922 ; 0.011 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1027 ; 0.304 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4811 ; 0.255 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2510 ; 0.101 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 321 ; 0.219 ; 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): 5 ; 0.088 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 37 ; 0.304 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 27 ; 0.222 ; 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): 2525 ; 0.784 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4126 ; 1.410 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1749 ; 2.638 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1713 ; 3.913 ; 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 4 A 33 REMARK 3 ORIGIN FOR THE GROUP (A): 42.6325 54.6322 17.9823 REMARK 3 T TENSOR REMARK 3 T11: 0.2104 T22: 0.3657 REMARK 3 T33: 0.2661 T12: -0.0337 REMARK 3 T13: -0.0751 T23: 0.0590 REMARK 3 L TENSOR REMARK 3 L11: 5.4623 L22: 13.7374 REMARK 3 L33: 7.8910 L12: -5.2962 REMARK 3 L13: -3.3860 L23: 8.9080 REMARK 3 S TENSOR REMARK 3 S11: -0.3549 S12: -0.0188 S13: -0.2329 REMARK 3 S21: 0.4860 S22: 0.2181 S23: 0.0002 REMARK 3 S31: 0.3468 S32: 0.2153 S33: 0.1367 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 : A 34 A 362 REMARK 3 ORIGIN FOR THE GROUP (A): 25.3996 62.3730 9.0667 REMARK 3 T TENSOR REMARK 3 T11: 0.0021 T22: 0.0854 REMARK 3 T33: 0.0447 T12: 0.0097 REMARK 3 T13: -0.0060 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 0.8363 L22: 1.7764 REMARK 3 L33: 0.7903 L12: -0.5993 REMARK 3 L13: -0.0837 L23: 0.0939 REMARK 3 S TENSOR REMARK 3 S11: 0.0094 S12: 0.0265 S13: 0.1189 REMARK 3 S21: -0.0226 S22: -0.0150 S23: -0.2781 REMARK 3 S31: -0.0153 S32: 0.2271 S33: 0.0056 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 : A 363 A 444 REMARK 3 ORIGIN FOR THE GROUP (A): 52.6622 62.2930 17.4329 REMARK 3 T TENSOR REMARK 3 T11: 0.1550 T22: 0.4760 REMARK 3 T33: 0.4210 T12: -0.0003 REMARK 3 T13: -0.0645 T23: 0.0658 REMARK 3 L TENSOR REMARK 3 L11: 3.1313 L22: 4.7393 REMARK 3 L33: 4.5982 L12: -0.4233 REMARK 3 L13: 1.0045 L23: 3.0807 REMARK 3 S TENSOR REMARK 3 S11: -0.0101 S12: 0.0007 S13: -0.0964 REMARK 3 S21: -0.0308 S22: 0.0672 S23: -0.4135 REMARK 3 S31: 0.1711 S32: 0.5097 S33: -0.0571 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1OLT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-AUG-03. REMARK 100 THE DEPOSITION ID IS D_1290013312. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.7420 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : 1440548 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 0.18200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP: 5 MICROL PROTEIN + 5 REMARK 280 MICROL RESEVOIR, PROTEIN: 10 MG/ML IN 10 MM HEPES PH 7.5, 3 MM REMARK 280 DTT, 150 MM NACL, 0.01% (V/V) C8E4 RESEVOIR: 22% (W/V) PEG10000, REMARK 280 100 MM HEPES PH 7.0, PH 7.00, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.22950 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 38.22950 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.22950 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 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 A2090 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 CARRIES OUT THE ANAEROBIC TRANSFORMATION OF REMARK 400 COPROPORPHYRINOGEN-III INTO PROTOPORPHYRINOGEN-IX. 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 SER A 2 REMARK 465 VAL A 3 REMARK 465 GLN A 14 REMARK 465 ASN A 17 REMARK 465 TYR A 18 REMARK 465 SER A 19 REMARK 465 GLY A 20 REMARK 465 PRO A 21 REMARK 465 ARG A 22 REMARK 465 ARG A 445 REMARK 465 GLN A 446 REMARK 465 LYS A 447 REMARK 465 ALA A 448 REMARK 465 ARG A 449 REMARK 465 MET A 450 REMARK 465 GLN A 451 REMARK 465 GLN A 452 REMARK 465 PHE A 453 REMARK 465 SER A 454 REMARK 465 ARG A 455 REMARK 465 VAL A 456 REMARK 465 ILE A 457 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 NZ LYS A 341 O HOH A 2349 1.61 REMARK 500 O HOH A 2086 O HOH A 2115 1.62 REMARK 500 OD2 ASP A 288 O HOH A 2324 2.09 REMARK 500 OD2 ASP A 288 O HOH A 2325 2.10 REMARK 500 O HOH A 2042 O HOH A 2140 2.11 REMARK 500 NH1 ARG A 365 O HOH A 2373 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 VAL A 94 CB VAL A 94 CG1 -0.127 REMARK 500 ARG A 184 CG ARG A 184 CD -0.152 REMARK 500 GLN A 186 CB GLN A 186 CG -0.204 REMARK 500 GLU A 188 CD GLU A 188 OE2 -0.066 REMARK 500 LYS A 266 CE LYS A 266 NZ 0.155 REMARK 500 GLU A 296 CD GLU A 296 OE2 0.073 REMARK 500 GLN A 345 CA GLN A 345 CB 0.136 REMARK 500 GLN A 345 CB GLN A 345 CG 0.226 REMARK 500 ALA A 397 CA ALA A 397 CB 0.167 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 131 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 180 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP A 288 CB - CG - OD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG A 292 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 294 CB - CG - OD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP A 295 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 365 NE - CZ - NH1 ANGL. DEV. = 3.3 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 SER A 25 155.06 142.09 REMARK 500 PRO A 148 47.10 -84.84 REMARK 500 GLN A 172 -62.77 73.29 REMARK 500 MET A 287 -110.86 59.38 REMARK 500 MET A 287 -86.59 69.44 REMARK 500 ASP A 288 -9.58 -143.81 REMARK 500 ASN A 309 -166.51 -128.30 REMARK 500 ASN A 309 -167.87 -126.94 REMARK 500 SER A 327 -2.98 71.90 REMARK 500 GLN A 340 129.73 -32.65 REMARK 500 GLN A 340 128.49 -32.65 REMARK 500 GLN A 340 125.10 -32.65 REMARK 500 GLN A 345 -72.10 -22.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2006 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2009 DISTANCE = 6.25 ANGSTROMS 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 SF4 A 500 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 62 SG REMARK 620 2 SF4 A 500 S2 113.9 REMARK 620 3 SF4 A 500 S3 124.2 104.1 REMARK 620 4 SF4 A 500 S4 101.3 110.3 101.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 500 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SAM A 501 N REMARK 620 2 SF4 A 500 S1 148.4 REMARK 620 3 SF4 A 500 S2 90.0 112.0 REMARK 620 4 SF4 A 500 S4 89.8 102.5 110.1 REMARK 620 5 SAM A 501 O 70.9 85.7 91.5 151.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 500 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 69 SG REMARK 620 2 SF4 A 500 S1 113.8 REMARK 620 3 SF4 A 500 S3 107.0 109.6 REMARK 620 4 SF4 A 500 S4 119.2 104.9 101.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 500 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 66 SG REMARK 620 2 SF4 A 500 S1 105.6 REMARK 620 3 SF4 A 500 S2 111.9 113.1 REMARK 620 4 SF4 A 500 S3 109.1 111.9 105.3 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 SAM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 500 DBREF 1OLT A 1 457 UNP P32131 HEMN_ECOLI 1 457 SEQADV 1OLT SER A 386 UNP P32131 ALA 386 CONFLICT SEQADV 1OLT GLN A 390 UNP P32131 LYS 390 CONFLICT SEQADV 1OLT LEU A 395 UNP P32131 HIS 395 CONFLICT SEQRES 1 A 457 MET SER VAL GLN GLN ILE ASP TRP ASP LEU ALA LEU ILE SEQRES 2 A 457 GLN LYS TYR ASN TYR SER GLY PRO ARG TYR THR SER TYR SEQRES 3 A 457 PRO THR ALA LEU GLU PHE SER GLU ASP PHE GLY GLU GLN SEQRES 4 A 457 ALA PHE LEU GLN ALA VAL ALA ARG TYR PRO GLU ARG PRO SEQRES 5 A 457 LEU SER LEU TYR VAL HIS ILE PRO PHE CYS HIS LYS LEU SEQRES 6 A 457 CYS TYR PHE CYS GLY CYS ASN LYS ILE VAL THR ARG GLN SEQRES 7 A 457 GLN HIS LYS ALA ASP GLN TYR LEU ASP ALA LEU GLU GLN SEQRES 8 A 457 GLU ILE VAL HIS ARG ALA PRO LEU PHE ALA GLY ARG HIS SEQRES 9 A 457 VAL SER GLN LEU HIS TRP GLY GLY GLY THR PRO THR TYR SEQRES 10 A 457 LEU ASN LYS ALA GLN ILE SER ARG LEU MET LYS LEU LEU SEQRES 11 A 457 ARG GLU ASN PHE GLN PHE ASN ALA ASP ALA GLU ILE SER SEQRES 12 A 457 ILE GLU VAL ASP PRO ARG GLU ILE GLU LEU ASP VAL LEU SEQRES 13 A 457 ASP HIS LEU ARG ALA GLU GLY PHE ASN ARG LEU SER MET SEQRES 14 A 457 GLY VAL GLN ASP PHE ASN LYS GLU VAL GLN ARG LEU VAL SEQRES 15 A 457 ASN ARG GLU GLN ASP GLU GLU PHE ILE PHE ALA LEU LEU SEQRES 16 A 457 ASN HIS ALA ARG GLU ILE GLY PHE THR SER THR ASN ILE SEQRES 17 A 457 ASP LEU ILE TYR GLY LEU PRO LYS GLN THR PRO GLU SER SEQRES 18 A 457 PHE ALA PHE THR LEU LYS ARG VAL ALA GLU LEU ASN PRO SEQRES 19 A 457 ASP ARG LEU SER VAL PHE ASN TYR ALA HIS LEU PRO THR SEQRES 20 A 457 ILE PHE ALA ALA GLN ARG LYS ILE LYS ASP ALA ASP LEU SEQRES 21 A 457 PRO SER PRO GLN GLN LYS LEU ASP ILE LEU GLN GLU THR SEQRES 22 A 457 ILE ALA PHE LEU THR GLN SER GLY TYR GLN PHE ILE GLY SEQRES 23 A 457 MET ASP HIS PHE ALA ARG PRO ASP ASP GLU LEU ALA VAL SEQRES 24 A 457 ALA GLN ARG GLU GLY VAL LEU HIS ARG ASN PHE GLN GLY SEQRES 25 A 457 TYR THR THR GLN GLY ASP THR ASP LEU LEU GLY MET GLY SEQRES 26 A 457 VAL SER ALA ILE SER MET ILE GLY ASP CYS TYR ALA GLN SEQRES 27 A 457 ASN GLN LYS GLU LEU LYS GLN TYR TYR GLN GLN VAL ASP SEQRES 28 A 457 GLU GLN GLY ASN ALA LEU TRP ARG GLY ILE ALA LEU THR SEQRES 29 A 457 ARG ASP ASP CYS ILE ARG ARG ASP VAL ILE LYS SER LEU SEQRES 30 A 457 ILE CYS ASN PHE ARG LEU ASP TYR SER PRO ILE GLU GLN SEQRES 31 A 457 GLN TRP ASP LEU LEU PHE ALA ASP TYR PHE ALA GLU ASP SEQRES 32 A 457 LEU LYS LEU LEU ALA PRO LEU ALA LYS ASP GLY LEU VAL SEQRES 33 A 457 ASP VAL ASP GLU LYS GLY ILE GLN VAL THR ALA LYS GLY SEQRES 34 A 457 ARG LEU LEU ILE ARG ASN ILE CYS MET CYS PHE ASP THR SEQRES 35 A 457 TYR LEU ARG GLN LYS ALA ARG MET GLN GLN PHE SER ARG SEQRES 36 A 457 VAL ILE HET SF4 A 500 8 HET SAM A 501 31 HET SAM A 502 35 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 2 SF4 FE4 S4 FORMUL 3 SAM 2(C15 H22 N6 O5 S) FORMUL 5 HOH *396(H2 O) HELIX 1 1 THR A 28 PHE A 32 5 5 HELIX 2 2 GLY A 37 ALA A 46 1 10 HELIX 3 3 GLN A 79 ALA A 97 1 19 HELIX 4 4 PRO A 98 ALA A 101 5 4 HELIX 5 5 THR A 114 LEU A 118 5 5 HELIX 6 6 ASN A 119 PHE A 134 1 16 HELIX 7 7 LEU A 153 GLU A 162 1 10 HELIX 8 8 ASN A 175 ASN A 183 1 9 HELIX 9 9 ASP A 187 ILE A 201 1 15 HELIX 10 10 THR A 218 ASN A 233 1 16 HELIX 11 11 PHE A 249 ILE A 255 5 7 HELIX 12 12 LYS A 256 LEU A 260 5 5 HELIX 13 13 SER A 262 SER A 280 1 19 HELIX 14 14 ASP A 295 GLY A 304 1 10 HELIX 15 15 GLU A 342 GLY A 354 1 13 HELIX 16 16 THR A 364 PHE A 381 1 18 HELIX 17 17 TYR A 385 TRP A 392 1 8 HELIX 18 18 LEU A 395 PHE A 400 1 6 HELIX 19 19 PHE A 400 ASP A 413 1 14 HELIX 20 20 GLY A 429 LEU A 431 5 3 HELIX 21 21 LEU A 432 CYS A 439 1 8 SHEET 1 AA 9 GLN A 283 GLY A 286 0 SHEET 2 AA 9 HIS A 289 ALA A 291 -1 O HIS A 289 N ILE A 285 SHEET 3 AA 9 ARG A 236 ASN A 241 -1 O LEU A 237 N PHE A 290 SHEET 4 AA 9 ASN A 207 TYR A 212 1 O ILE A 208 N SER A 238 SHEET 5 AA 9 ARG A 166 GLN A 172 1 O LEU A 167 N ASN A 207 SHEET 6 AA 9 PHE A 136 VAL A 146 1 O ILE A 144 N SER A 168 SHEET 7 AA 9 VAL A 105 GLY A 112 1 O VAL A 105 N ASN A 137 SHEET 8 AA 9 LEU A 53 ILE A 59 1 O LEU A 53 N SER A 106 SHEET 9 AA 9 ASP A 320 MET A 324 1 O ASP A 320 N SER A 54 SHEET 1 AB 2 PHE A 61 CYS A 62 0 SHEET 2 AB 2 ILE A 74 VAL A 75 1 O ILE A 74 N CYS A 62 SHEET 1 AC 2 HIS A 307 ARG A 308 0 SHEET 2 AC 2 TYR A 313 THR A 314 -1 O THR A 314 N HIS A 307 SHEET 1 AD 3 ILE A 329 ILE A 332 0 SHEET 2 AD 3 CYS A 335 ASN A 339 -1 O CYS A 335 N ILE A 332 SHEET 3 AD 3 LEU A 357 ALA A 362 -1 N TRP A 358 O GLN A 338 SHEET 1 AE 3 ARG A 382 ASP A 384 0 SHEET 2 AE 3 GLY A 422 VAL A 425 -1 O ILE A 423 N LEU A 383 SHEET 3 AE 3 VAL A 416 VAL A 418 -1 O ASP A 417 N GLN A 424 LINK FE1 SF4 A 500 SG CYS A 62 1555 1555 2.32 LINK FE3 SF4 A 500 N SAM A 501 1555 1555 2.55 LINK FE3 SF4 A 500 O SAM A 501 1555 1555 2.24 LINK FE2 SF4 A 500 SG CYS A 69 1555 1555 2.35 LINK FE4 SF4 A 500 SG CYS A 66 1555 1555 2.49 CISPEP 1 TYR A 26 PRO A 27 0 -5.69 CISPEP 2 GLY A 112 GLY A 113 0 8.32 SITE 1 AC1 23 PHE A 68 CYS A 69 GLY A 70 CYS A 71 SITE 2 AC1 23 GLY A 112 GLY A 113 THR A 114 GLU A 145 SITE 3 AC1 23 VAL A 146 ASP A 147 GLY A 170 GLN A 172 SITE 4 AC1 23 ARG A 184 ASP A 209 ILE A 211 PHE A 240 SITE 5 AC1 23 ASN A 241 TYR A 242 ALA A 243 GLN A 252 SITE 6 AC1 23 SF4 A 500 SAM A 502 HOH A2179 SITE 1 AC2 18 TYR A 56 HIS A 58 GLY A 111 GLY A 112 SITE 2 AC2 18 GLU A 145 PHE A 240 PHE A 310 GLN A 311 SITE 3 AC2 18 SER A 327 ALA A 328 ILE A 329 SAM A 501 SITE 4 AC2 18 HOH A2342 HOH A2391 HOH A2392 HOH A2393 SITE 5 AC2 18 HOH A2394 HOH A2396 SITE 1 AC3 10 CYS A 62 CYS A 66 PHE A 68 CYS A 69 SITE 2 AC3 10 LYS A 73 GLY A 113 THR A 114 ARG A 149 SITE 3 AC3 10 ARG A 184 SAM A 501 CRYST1 114.036 114.036 76.459 90.00 90.00 120.00 P 63 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 0.008769 0.005063 0.000000 0.00000 SCALE2 0.000000 0.010126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013079 0.00000