HEADER OXIDOREDUCTASE 06-JUN-23 8JNC TITLE CRYSTAL STRUCTURE OF CYTOCHROME P450 IKAD FROM STREPTOMYCES SP. ZJ306, TITLE 2 IN COMPLEX WITH THE SUBSTRATE 10-EPI-MALTOPHILIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES SP. ZJ306; SOURCE 3 ORGANISM_TAXID: 1469403; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HYDROXYLATION, POLYCYCLIC TETRAMATE MACROLACTAM, OXIDOREDUCTASE, KEYWDS 2 CYTOCHROME P450 EXPDTA X-RAY DIFFRACTION AUTHOR Y.L.ZHANG,L.P.ZHANG,C.S.ZHANG REVDAT 2 20-DEC-23 8JNC 1 JRNL REVDAT 1 15-NOV-23 8JNC 0 JRNL AUTH P.JIANG,H.JIN,G.ZHANG,W.ZHANG,W.LIU,Y.ZHU,C.ZHANG,L.ZHANG JRNL TITL A MECHANISTIC UNDERSTANDING OF THE DISTINCT REGIO- AND JRNL TITL 2 CHEMOSELECTIVITY OF MULTIFUNCTIONAL P450S BY STRUCTURAL JRNL TITL 3 COMPARISON OF IKAD AND CFTA COMPLEXED WITH COMMON JRNL TITL 4 SUBSTRATES. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 62 10728 2023 JRNL REFN ESSN 1521-3773 JRNL PMID 37917570 JRNL DOI 10.1002/ANIE.202310728 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 71307 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 3618 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 13.2900 - 5.7700 0.97 2599 158 0.1830 0.1854 REMARK 3 2 5.7600 - 4.6400 0.99 2625 137 0.1612 0.1799 REMARK 3 3 4.6400 - 4.0700 0.99 2647 143 0.1460 0.1919 REMARK 3 4 4.0700 - 3.7100 1.00 2622 131 0.1522 0.1847 REMARK 3 5 3.7100 - 3.4500 1.00 2617 138 0.1665 0.1663 REMARK 3 6 3.4500 - 3.2500 1.00 2625 135 0.1763 0.2143 REMARK 3 7 3.2500 - 3.0900 1.00 2625 149 0.1955 0.2630 REMARK 3 8 3.0900 - 2.9600 1.00 2581 154 0.2132 0.2281 REMARK 3 9 2.9500 - 2.8400 1.00 2616 141 0.2118 0.2989 REMARK 3 10 2.8400 - 2.7500 1.00 2654 125 0.2072 0.2945 REMARK 3 11 2.7500 - 2.6600 1.00 2619 137 0.2063 0.2797 REMARK 3 12 2.6600 - 2.5800 1.00 2613 156 0.1937 0.2403 REMARK 3 13 2.5800 - 2.5200 1.00 2599 137 0.1874 0.2506 REMARK 3 14 2.5200 - 2.4600 1.00 2611 142 0.1833 0.2381 REMARK 3 15 2.4600 - 2.4000 1.00 2612 134 0.1801 0.2550 REMARK 3 16 2.4000 - 2.3500 1.00 2605 121 0.1905 0.2556 REMARK 3 17 2.3500 - 2.3000 1.00 2632 123 0.1894 0.2157 REMARK 3 18 2.3000 - 2.2600 1.00 2603 147 0.1912 0.2600 REMARK 3 19 2.2600 - 2.2200 1.00 2640 135 0.1941 0.2290 REMARK 3 20 2.2200 - 2.1800 1.00 2584 134 0.1994 0.2544 REMARK 3 21 2.1800 - 2.1500 0.99 2594 134 0.2071 0.2661 REMARK 3 22 2.1500 - 2.1100 0.99 2589 126 0.2192 0.2613 REMARK 3 23 2.1100 - 2.0800 0.99 2597 134 0.2253 0.2896 REMARK 3 24 2.0800 - 2.0500 0.98 2528 147 0.2355 0.2941 REMARK 3 25 2.0500 - 2.0300 0.98 2552 145 0.2489 0.2907 REMARK 3 26 2.0300 - 2.0000 0.97 2500 155 0.2468 0.2970 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 6439 REMARK 3 ANGLE : 1.335 8792 REMARK 3 CHIRALITY : 0.059 958 REMARK 3 PLANARITY : 0.011 1156 REMARK 3 DIHEDRAL : 8.264 947 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8JNC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 14-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038261. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO 171.39.7E REMARK 200 DATA SCALING SOFTWARE : AIMLESS CCP4INTERFACE 7.0.073 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71321 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 13.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.16200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.64700 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: MOLREP CCP4INTERFACE 7.0.073 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5-4 M SODIUM FORMATE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-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 -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 40.55510 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.97400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 71.71656 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.55510 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.97400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 71.71656 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 TOTAL BURIED SURFACE AREA: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 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 TOTAL BURIED SURFACE AREA: 1240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL 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 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 910 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1005 LIES ON A SPECIAL POSITION. 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 PRO A 2 REMARK 465 GLY A 3 REMARK 465 GLN A 4 REMARK 465 GLN A 5 REMARK 465 GLU A 6 REMARK 465 GLN A 7 REMARK 465 GLN A 8 REMARK 465 ALA A 9 REMARK 465 PRO A 10 REMARK 465 SER A 11 REMARK 465 GLU A 12 REMARK 465 HIS A 13 REMARK 465 PRO A 14 REMARK 465 GLU A 15 REMARK 465 GLN A 16 REMARK 465 GLN A 17 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 GLY B 3 REMARK 465 GLN B 4 REMARK 465 GLN B 5 REMARK 465 GLU B 6 REMARK 465 GLN B 7 REMARK 465 GLN B 8 REMARK 465 ALA B 9 REMARK 465 PRO B 10 REMARK 465 SER B 11 REMARK 465 GLU B 12 REMARK 465 HIS B 13 REMARK 465 PRO B 14 REMARK 465 GLU B 15 REMARK 465 GLN B 16 REMARK 465 GLN B 17 REMARK 465 GLU B 18 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 ALA A 89 CB REMARK 470 ARG A 112 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 167 CG CD OE1 OE2 REMARK 470 PRO A 168 CG CD REMARK 470 ARG A 192 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 195 CG CD OE1 NE2 REMARK 470 ASP A 214 CG OD1 OD2 REMARK 470 ARG A 394 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 47 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 112 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 118 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 167 CG CD OE1 OE2 REMARK 470 ARG B 192 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 229 CG CD NE CZ NH1 NH2 REMARK 470 SER B 293 OG REMARK 470 GLU B 341 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 787 O HOH A 906 2.03 REMARK 500 O HOH B 1001 O HOH B 1003 2.04 REMARK 500 OD2 ASP B 169 OH TYR B 200 2.05 REMARK 500 O HOH B 623 O HOH B 787 2.06 REMARK 500 O HOH B 664 O HOH B 950 2.10 REMARK 500 O HOH B 785 O HOH B 843 2.10 REMARK 500 O HOH B 655 O HOH B 965 2.11 REMARK 500 O HOH A 635 O HOH A 784 2.12 REMARK 500 O GLY A 344 O HOH A 601 2.12 REMARK 500 O HOH B 744 O HOH B 863 2.12 REMARK 500 O TRP A 408 O HOH A 602 2.15 REMARK 500 O HOH A 669 O HOH A 1011 2.15 REMARK 500 O HOH A 891 O HOH A 973 2.15 REMARK 500 O HOH B 842 O HOH B 947 2.16 REMARK 500 O HOH B 813 O HOH B 817 2.16 REMARK 500 O HOH A 720 O HOH A 739 2.16 REMARK 500 OE1 GLU A 226 O HOH A 603 2.17 REMARK 500 O HOH B 929 O HOH B 988 2.17 REMARK 500 O HOH B 770 O HOH B 926 2.18 REMARK 500 O HOH B 605 O HOH B 741 2.18 REMARK 500 OD2 ASP B 81 O HOH B 601 2.18 REMARK 500 O HOH A 965 O HOH A 1025 2.19 REMARK 500 O HOH A 843 O HOH A 924 2.19 REMARK 500 O HOH A 829 O HOH A 978 2.19 REMARK 500 O HOH B 921 O HOH B 989 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 876 O HOH B 938 2555 2.07 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 B 382 NE - CZ - NH2 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 LEU A 150 -52.37 -135.64 REMARK 500 ARG A 211 82.32 106.41 REMARK 500 PHE A 247 -31.43 -140.10 REMARK 500 ARG A 267 -122.26 46.48 REMARK 500 SER A 296 -91.42 -100.19 REMARK 500 SER A 308 54.24 38.21 REMARK 500 LEU B 150 -53.03 -133.43 REMARK 500 PHE B 247 -33.47 -131.55 REMARK 500 ARG B 267 -117.22 53.70 REMARK 500 SER B 296 -81.32 -94.15 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 A1035 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A1036 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH A1037 DISTANCE = 6.83 ANGSTROMS REMARK 525 HOH A1038 DISTANCE = 6.92 ANGSTROMS REMARK 525 HOH B1005 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH B1006 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH B1007 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH B1008 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH B1009 DISTANCE = 6.87 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 HEM A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 357 SG REMARK 620 2 HEM A 501 NA 105.5 REMARK 620 3 HEM A 501 NB 93.3 87.9 REMARK 620 4 HEM A 501 NC 92.7 161.6 88.0 REMARK 620 5 HEM A 501 ND 103.0 87.8 163.7 91.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 505 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN B 352 O REMARK 620 2 HEM B 501 O1A 139.3 REMARK 620 3 HOH B 708 O 54.1 87.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 357 SG REMARK 620 2 HEM B 501 NA 105.7 REMARK 620 3 HEM B 501 NB 93.3 88.2 REMARK 620 4 HEM B 501 NC 90.7 163.6 91.5 REMARK 620 5 HEM B 501 ND 101.1 87.3 165.6 89.0 REMARK 620 N 1 2 3 4 DBREF1 8JNC A 1 408 UNP A0A0B4ZV78_9ACTN DBREF2 8JNC A A0A0B4ZV78 59 466 DBREF1 8JNC B 1 408 UNP A0A0B4ZV78_9ACTN DBREF2 8JNC B A0A0B4ZV78 59 466 SEQRES 1 A 408 MET PRO GLY GLN GLN GLU GLN GLN ALA PRO SER GLU HIS SEQRES 2 A 408 PRO GLU GLN GLN GLU LEU LEU THR PHE PRO PHE ALA SER SEQRES 3 A 408 THR GLY LEU GLU PHE PRO PRO VAL TYR HIS GLU LEU TYR SEQRES 4 A 408 GLN GLN ARG LEU THR LYS VAL ARG LEU PRO TYR GLY ASP SEQRES 5 A 408 ASP ALA TYR LEU ALA ILE ARG TYR ALA ASP VAL LYS THR SEQRES 6 A 408 VAL LEU SER ASP SER ARG PHE SER ILE VAL ALA SER LEU SEQRES 7 A 408 GLY GLN ASP GLN PRO ARG THR ARG ALA GLY ALA ARG VAL SEQRES 8 A 408 GLY ASN GLY LEU PHE SER LEU ASP PRO PRO GLN HIS SER SEQRES 9 A 408 ARG LEU ARG SER VAL LEU GLY ARG ASP PHE THR PRO ARG SEQRES 10 A 408 ARG VAL GLU LYS LEU ARG GLU ARG VAL ARG GLU LEU THR SEQRES 11 A 408 ASP GLN CYS LEU ASP ARG MET GLU ALA ALA GLY SER PRO SEQRES 12 A 408 ALA ASP LEU VAL ALA HIS LEU ALA VAL PRO MET PRO THR SEQRES 13 A 408 ALA VAL VAL CYS GLU MET MET GLY VAL PRO GLU PRO ASP SEQRES 14 A 408 HIS HIS LEU PHE TRP GLY TRP ALA GLU THR ILE LEU SER SEQRES 15 A 408 ASN ASP THR THR PRO ASP ASP LEU ILE ARG ARG TYR GLN SEQRES 16 A 408 GLU PHE THR ALA TYR MET GLY ALA MET VAL GLU GLU ARG SEQRES 17 A 408 ARG ALA ARG PRO THR ASP ASP MET PHE GLY MET LEU VAL SEQRES 18 A 408 ARG ALA CYS ASP GLU GLU GLY ARG ILE THR GLU ILE GLU SEQRES 19 A 408 MET HIS ALA LEU ALA SER ASP LEU LEU SER ALA GLY PHE SEQRES 20 A 408 VAL SER THR ALA HIS GLN ILE ALA ASN PHE THR ALA MET SEQRES 21 A 408 LEU LEU ALA ARG PRO GLU ARG LEU GLN PRO LEU VAL ASP SEQRES 22 A 408 LYS PRO GLU GLN ILE PRO ALA ALA VAL GLU GLU LEU MET SEQRES 23 A 408 ARG HIS VAL PRO ILE LEU SER GLY PHE SER PHE PRO ARG SEQRES 24 A 408 TYR ALA THR GLU ASP LEU GLU MET SER GLY VAL THR VAL SEQRES 25 A 408 ARG ARG GLY GLU ALA VAL ILE PRO VAL ILE ALA ALA ALA SEQRES 26 A 408 ASN ARG ASP PRO ASP VAL TYR PRO ASP ALA GLY ARG LEU SEQRES 27 A 408 ASP LEU GLU ARG ASN GLY LEU PRO HIS LEU GLY PHE GLY SEQRES 28 A 408 GLN GLY PRO HIS PHE CYS ILE GLY ALA HIS LEU ALA ARG SEQRES 29 A 408 VAL GLU LEU GLN VAL VAL LEU GLU ALA LEU THR GLU ARG SEQRES 30 A 408 PHE PRO ASP LEU ARG PHE GLY ILE PRO GLU ASN ALA LEU SEQRES 31 A 408 LYS TRP LYS ARG GLY HIS PHE MET ASN GLY LEU HIS GLU SEQRES 32 A 408 LEU PRO VAL ALA TRP SEQRES 1 B 408 MET PRO GLY GLN GLN GLU GLN GLN ALA PRO SER GLU HIS SEQRES 2 B 408 PRO GLU GLN GLN GLU LEU LEU THR PHE PRO PHE ALA SER SEQRES 3 B 408 THR GLY LEU GLU PHE PRO PRO VAL TYR HIS GLU LEU TYR SEQRES 4 B 408 GLN GLN ARG LEU THR LYS VAL ARG LEU PRO TYR GLY ASP SEQRES 5 B 408 ASP ALA TYR LEU ALA ILE ARG TYR ALA ASP VAL LYS THR SEQRES 6 B 408 VAL LEU SER ASP SER ARG PHE SER ILE VAL ALA SER LEU SEQRES 7 B 408 GLY GLN ASP GLN PRO ARG THR ARG ALA GLY ALA ARG VAL SEQRES 8 B 408 GLY ASN GLY LEU PHE SER LEU ASP PRO PRO GLN HIS SER SEQRES 9 B 408 ARG LEU ARG SER VAL LEU GLY ARG ASP PHE THR PRO ARG SEQRES 10 B 408 ARG VAL GLU LYS LEU ARG GLU ARG VAL ARG GLU LEU THR SEQRES 11 B 408 ASP GLN CYS LEU ASP ARG MET GLU ALA ALA GLY SER PRO SEQRES 12 B 408 ALA ASP LEU VAL ALA HIS LEU ALA VAL PRO MET PRO THR SEQRES 13 B 408 ALA VAL VAL CYS GLU MET MET GLY VAL PRO GLU PRO ASP SEQRES 14 B 408 HIS HIS LEU PHE TRP GLY TRP ALA GLU THR ILE LEU SER SEQRES 15 B 408 ASN ASP THR THR PRO ASP ASP LEU ILE ARG ARG TYR GLN SEQRES 16 B 408 GLU PHE THR ALA TYR MET GLY ALA MET VAL GLU GLU ARG SEQRES 17 B 408 ARG ALA ARG PRO THR ASP ASP MET PHE GLY MET LEU VAL SEQRES 18 B 408 ARG ALA CYS ASP GLU GLU GLY ARG ILE THR GLU ILE GLU SEQRES 19 B 408 MET HIS ALA LEU ALA SER ASP LEU LEU SER ALA GLY PHE SEQRES 20 B 408 VAL SER THR ALA HIS GLN ILE ALA ASN PHE THR ALA MET SEQRES 21 B 408 LEU LEU ALA ARG PRO GLU ARG LEU GLN PRO LEU VAL ASP SEQRES 22 B 408 LYS PRO GLU GLN ILE PRO ALA ALA VAL GLU GLU LEU MET SEQRES 23 B 408 ARG HIS VAL PRO ILE LEU SER GLY PHE SER PHE PRO ARG SEQRES 24 B 408 TYR ALA THR GLU ASP LEU GLU MET SER GLY VAL THR VAL SEQRES 25 B 408 ARG ARG GLY GLU ALA VAL ILE PRO VAL ILE ALA ALA ALA SEQRES 26 B 408 ASN ARG ASP PRO ASP VAL TYR PRO ASP ALA GLY ARG LEU SEQRES 27 B 408 ASP LEU GLU ARG ASN GLY LEU PRO HIS LEU GLY PHE GLY SEQRES 28 B 408 GLN GLY PRO HIS PHE CYS ILE GLY ALA HIS LEU ALA ARG SEQRES 29 B 408 VAL GLU LEU GLN VAL VAL LEU GLU ALA LEU THR GLU ARG SEQRES 30 B 408 PHE PRO ASP LEU ARG PHE GLY ILE PRO GLU ASN ALA LEU SEQRES 31 B 408 LYS TRP LYS ARG GLY HIS PHE MET ASN GLY LEU HIS GLU SEQRES 32 B 408 LEU PRO VAL ALA TRP HET HEM A 501 73 HET E5I A 502 75 HET FMT A 503 4 HET FMT A 504 5 HET HEM B 501 73 HET E5I B 502 75 HET FMT B 503 4 HET FMT B 504 4 HET NA B 505 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM E5I (1Z,3E,5S,8R,9S,10S,11R,13R,15R,16S,18Z,24S,25S)-11- HETNAM 2 E5I ETHYL-2,24-DIHYDROXY-10-METHYL-21,26- HETNAM 3 E5I DIAZAPENTACYCLO[23.2.1.09,13.08,15.05,16]OCTACOSA- HETNAM 4 E5I 1(2),3,18-TRIENE-7,20,27,28-TETRAONE HETNAM FMT FORMIC ACID HETNAM NA SODIUM ION HETSYN HEM HEME HETSYN E5I 10-EPI-MALTOPHILIN FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 E5I 2(C29 H38 N2 O6) FORMUL 5 FMT 4(C H2 O2) FORMUL 11 NA NA 1+ FORMUL 12 HOH *847(H2 O) HELIX 1 AA1 PRO A 33 GLN A 40 1 8 HELIX 2 AA2 ARG A 59 ASP A 69 1 11 HELIX 3 AA3 GLY A 94 LEU A 98 5 5 HELIX 4 AA4 PRO A 101 ARG A 112 1 12 HELIX 5 AA5 THR A 115 GLU A 120 1 6 HELIX 6 AA6 LEU A 122 GLY A 141 1 20 HELIX 7 AA7 LEU A 146 LEU A 150 1 5 HELIX 8 AA8 VAL A 152 GLY A 164 1 13 HELIX 9 AA9 PRO A 166 PRO A 168 5 3 HELIX 10 AB1 ASP A 169 SER A 182 1 14 HELIX 11 AB2 THR A 186 ALA A 210 1 25 HELIX 12 AB3 ASP A 215 GLU A 226 1 12 HELIX 13 AB4 THR A 231 GLY A 246 1 16 HELIX 14 AB5 PHE A 247 ALA A 263 1 17 HELIX 15 AB6 LEU A 268 LYS A 274 1 7 HELIX 16 AB7 GLN A 277 VAL A 289 1 13 HELIX 17 AB8 VAL A 321 ASN A 326 1 6 HELIX 18 AB9 GLN A 352 PHE A 356 5 5 HELIX 19 AC1 GLY A 359 PHE A 378 1 20 HELIX 20 AC2 PRO A 386 LEU A 390 5 5 HELIX 21 AC3 PRO B 33 TYR B 39 1 7 HELIX 22 AC4 ARG B 59 ASP B 69 1 11 HELIX 23 AC5 GLY B 94 LEU B 98 5 5 HELIX 24 AC6 PRO B 101 ARG B 112 1 12 HELIX 25 AC7 THR B 115 GLU B 120 1 6 HELIX 26 AC8 LEU B 122 GLY B 141 1 20 HELIX 27 AC9 LEU B 146 LEU B 150 1 5 HELIX 28 AD1 VAL B 152 GLY B 164 1 13 HELIX 29 AD2 PRO B 166 PRO B 168 5 3 HELIX 30 AD3 ASP B 169 SER B 182 1 14 HELIX 31 AD4 THR B 186 ARG B 211 1 26 HELIX 32 AD5 ASP B 215 GLU B 226 1 12 HELIX 33 AD6 THR B 231 GLY B 246 1 16 HELIX 34 AD7 PHE B 247 ALA B 263 1 17 HELIX 35 AD8 LEU B 268 LYS B 274 1 7 HELIX 36 AD9 GLN B 277 VAL B 289 1 13 HELIX 37 AE1 VAL B 321 ASN B 326 1 6 HELIX 38 AE2 GLN B 352 PHE B 356 5 5 HELIX 39 AE3 GLY B 359 PHE B 378 1 20 HELIX 40 AE4 PRO B 386 LEU B 390 5 5 SHEET 1 AA1 6 LEU A 20 THR A 21 0 SHEET 2 AA1 6 THR A 44 ARG A 47 1 O ARG A 47 N LEU A 20 SHEET 3 AA1 6 ALA A 54 ALA A 57 -1 O ALA A 54 N VAL A 46 SHEET 4 AA1 6 ALA A 317 PRO A 320 1 O ILE A 319 N TYR A 55 SHEET 5 AA1 6 ARG A 299 ALA A 301 -1 N ARG A 299 O VAL A 318 SHEET 6 AA1 6 PHE A 72 SER A 73 -1 N SER A 73 O TYR A 300 SHEET 1 AA2 3 ALA A 144 ASP A 145 0 SHEET 2 AA2 3 PRO A 405 ALA A 407 -1 O VAL A 406 N ALA A 144 SHEET 3 AA2 3 ARG A 382 PHE A 383 -1 N ARG A 382 O ALA A 407 SHEET 1 AA3 2 LEU A 305 MET A 307 0 SHEET 2 AA3 2 VAL A 310 VAL A 312 -1 O VAL A 312 N LEU A 305 SHEET 1 AA4 6 LEU B 20 THR B 21 0 SHEET 2 AA4 6 THR B 44 ARG B 47 1 O ARG B 47 N LEU B 20 SHEET 3 AA4 6 ALA B 54 ALA B 57 -1 O ALA B 54 N VAL B 46 SHEET 4 AA4 6 ALA B 317 PRO B 320 1 O ILE B 319 N TYR B 55 SHEET 5 AA4 6 ARG B 299 ALA B 301 -1 N ARG B 299 O VAL B 318 SHEET 6 AA4 6 PHE B 72 SER B 73 -1 N SER B 73 O TYR B 300 SHEET 1 AA5 3 ALA B 144 ASP B 145 0 SHEET 2 AA5 3 PRO B 405 ALA B 407 -1 O VAL B 406 N ALA B 144 SHEET 3 AA5 3 ARG B 382 PHE B 383 -1 N ARG B 382 O ALA B 407 SHEET 1 AA6 2 LEU B 305 MET B 307 0 SHEET 2 AA6 2 VAL B 310 VAL B 312 -1 O VAL B 312 N LEU B 305 LINK SG CYS A 357 FE HEM A 501 1555 1555 2.29 LINK O GLN B 352 NA NA B 505 1555 1555 2.91 LINK SG CYS B 357 FE HEM B 501 1555 1555 2.37 LINK O1A HEM B 501 NA NA B 505 1555 1555 2.74 LINK NA NA B 505 O HOH B 708 1555 1555 2.97 CISPEP 1 PHE A 22 PRO A 23 0 5.32 CISPEP 2 PRO A 100 PRO A 101 0 -0.36 CISPEP 3 SER A 142 PRO A 143 0 0.89 CISPEP 4 PHE B 22 PRO B 23 0 3.29 CISPEP 5 PRO B 100 PRO B 101 0 3.97 CISPEP 6 SER B 142 PRO B 143 0 -6.37 CRYST1 91.895 81.948 143.838 90.00 94.30 90.00 I 1 2 1 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 0.010882 0.000000 0.000819 0.00000 SCALE2 0.000000 0.012203 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006972 0.00000