HEADER OXIDOREDUCTASE 02-DEC-09 3KX3 TITLE CRYSTAL STRUCTURE OF BACILLUS MEGATERIUM BM3 HEME DOMAIN MUTANT L86E COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL P-450/NADPH-P450 REDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: HEME DOMAIN (UNP RESIDUES 2-471); COMPND 5 SYNONYM: FLAVOCYTOCHROME P450 BM3, CYTOCHROME P450(BM-3), P450BM-3, COMPND 6 CYTOCHROME P450 102, NADPH--CYTOCHROME P450 REDUCTASE; COMPND 7 EC: 1.14.14.1; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS MEGATERIUM; SOURCE 3 ORGANISM_TAXID: 1404; SOURCE 4 GENE: CYP102A1, CYP102; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: TG1 KEYWDS CYTOCHROME P450, L86E MUTANT, HEME DOMAIN, CYTOPLASM, ELECTRON KEYWDS 2 TRANSPORT, FAD, FLAVOPROTEIN, FMN, HEME, IRON, METAL-BINDING, KEYWDS 3 MONOOXYGENASE, MULTIFUNCTIONAL ENZYME, NADP, OXIDOREDUCTASE, KEYWDS 4 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR H.M.GIRVAN,C.W.LEVY,D.LEYS,A.W.MUNRO REVDAT 3 29-MAY-24 3KX3 1 REMARK REVDAT 2 10-NOV-21 3KX3 1 REMARK SEQADV LINK REVDAT 1 19-MAY-10 3KX3 0 JRNL AUTH H.M.GIRVAN,C.W.LEVY,P.WILLIAMS,K.FISHER,M.R.CHEESMAN, JRNL AUTH 2 S.E.RIGBY,D.LEYS,A.W.MUNRO JRNL TITL GLUTAMATE-HAEM ESTER BOND FORMATION IS DISFAVOURED IN JRNL TITL 2 FLAVOCYTOCHROME P450 BM3: CHARACTERIZATION OF GLUTAMATE JRNL TITL 3 SUBSTITUTION MUTANTS AT THE HAEM SITE OF P450 BM3. JRNL REF BIOCHEM.J. V. 427 455 2010 JRNL REFN ISSN 0264-6021 JRNL PMID 20180779 JRNL DOI 10.1042/BJ20091603 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 96306 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4812 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 39.4191 - 5.5958 0.84 2713 140 0.1821 0.2130 REMARK 3 2 5.5958 - 4.4435 0.92 2945 146 0.1399 0.1824 REMARK 3 3 4.4435 - 3.8824 0.92 2943 142 0.1208 0.1849 REMARK 3 4 3.8824 - 3.5277 0.92 2931 151 0.1242 0.1529 REMARK 3 5 3.5277 - 3.2750 0.92 2957 135 0.1238 0.1858 REMARK 3 6 3.2750 - 3.0820 0.93 2942 174 0.1378 0.1680 REMARK 3 7 3.0820 - 2.9277 0.94 2929 182 0.1470 0.1831 REMARK 3 8 2.9277 - 2.8003 0.94 2961 169 0.1477 0.1960 REMARK 3 9 2.8003 - 2.6925 0.95 3027 164 0.1417 0.2062 REMARK 3 10 2.6925 - 2.5996 0.96 3033 164 0.1446 0.1948 REMARK 3 11 2.5996 - 2.5183 0.97 3084 157 0.1408 0.1989 REMARK 3 12 2.5183 - 2.4463 0.97 3043 168 0.1453 0.1981 REMARK 3 13 2.4463 - 2.3820 0.97 3094 151 0.1411 0.1893 REMARK 3 14 2.3820 - 2.3238 0.97 3098 182 0.1396 0.2004 REMARK 3 15 2.3238 - 2.2710 0.98 3089 149 0.1347 0.1958 REMARK 3 16 2.2710 - 2.2227 0.98 3088 164 0.1378 0.1768 REMARK 3 17 2.2227 - 2.1782 0.99 3120 166 0.1381 0.2067 REMARK 3 18 2.1782 - 2.1371 0.99 3151 146 0.1305 0.1846 REMARK 3 19 2.1371 - 2.0990 0.99 3168 142 0.1336 0.1858 REMARK 3 20 2.0990 - 2.0634 0.99 3120 159 0.1347 0.1776 REMARK 3 21 2.0634 - 2.0301 0.99 3131 173 0.1346 0.1980 REMARK 3 22 2.0301 - 1.9989 0.99 3202 154 0.1421 0.1945 REMARK 3 23 1.9989 - 1.9695 0.99 3074 173 0.1441 0.2023 REMARK 3 24 1.9695 - 1.9417 1.00 3171 174 0.1383 0.2014 REMARK 3 25 1.9417 - 1.9155 1.00 3153 168 0.1463 0.1971 REMARK 3 26 1.9155 - 1.8906 1.00 3150 174 0.1491 0.2230 REMARK 3 27 1.8906 - 1.8670 1.00 3160 162 0.1579 0.2325 REMARK 3 28 1.8670 - 1.8445 1.00 3107 174 0.1493 0.1886 REMARK 3 29 1.8445 - 1.8231 1.00 3182 157 0.1573 0.2154 REMARK 3 30 1.8231 - 1.8026 0.86 2728 152 0.1666 0.2125 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 : 0.34 REMARK 3 B_SOL : 58.92 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.630 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) : -2.85360 REMARK 3 B22 (A**2) : -0.51220 REMARK 3 B33 (A**2) : 3.36570 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.87890 REMARK 3 B23 (A**2) : 0.00000 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 : 0.025 7731 REMARK 3 ANGLE : 2.095 10487 REMARK 3 CHIRALITY : 0.157 1106 REMARK 3 PLANARITY : 0.011 1374 REMARK 3 DIHEDRAL : 17.601 2915 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 3KX3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056555. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0698 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 100096 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.803 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM CACODYLIC ACID, PH 6.0, 16% PEG REMARK 280 3350, 140MM MGCL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K, PH 7.4 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 74.12500 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 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 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 THR A 1 REMARK 465 ILE A 2 REMARK 465 GLY A 227 REMARK 465 GLU A 228 REMARK 465 PRO A 459 REMARK 465 SER A 460 REMARK 465 PRO A 461 REMARK 465 SER A 462 REMARK 465 THR A 463 REMARK 465 GLU A 464 REMARK 465 GLN A 465 REMARK 465 SER A 466 REMARK 465 ALA A 467 REMARK 465 LYS A 468 REMARK 465 LYS A 469 REMARK 465 VAL A 470 REMARK 465 THR B 1 REMARK 465 ILE B 2 REMARK 465 PRO B 459 REMARK 465 SER B 460 REMARK 465 PRO B 461 REMARK 465 SER B 462 REMARK 465 THR B 463 REMARK 465 GLU B 464 REMARK 465 GLN B 465 REMARK 465 SER B 466 REMARK 465 ALA B 467 REMARK 465 LYS B 468 REMARK 465 LYS B 469 REMARK 465 VAL B 470 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 3 CG CD CE NZ REMARK 470 GLU A 4 CG CD OE1 OE2 REMARK 470 GLN A 229 CG CD OE1 NE2 REMARK 470 GLU A 373 CG CD OE1 OE2 REMARK 470 GLU B 228 CG CD OE1 OE2 REMARK 470 GLN B 229 CG CD OE1 NE2 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 O2 140 B 1470 O HOH B 566 2.01 REMARK 500 O2 140 A 1470 O HOH A 660 2.04 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 TRP B 96 CG TRP B 96 CD1 0.086 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 ASP A 68 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ASP A 121 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 250 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 250 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG B 50 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG B 50 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP B 63 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 63 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 LEU B 104 CB - CG - CD1 ANGL. DEV. = 10.8 DEGREES REMARK 500 ASP B 232 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP B 250 CB - CG - OD1 ANGL. DEV. = 5.7 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 LYS A 15 -125.97 51.52 REMARK 500 HIS A 266 -28.31 -141.74 REMARK 500 ASP A 370 36.18 -85.43 REMARK 500 THR A 436 55.53 -142.35 REMARK 500 LEU A 437 -64.87 70.26 REMARK 500 LYS B 15 -125.71 54.85 REMARK 500 ASP B 84 39.00 -94.76 REMARK 500 ASP B 232 -166.90 -127.81 REMARK 500 HIS B 266 -31.31 -142.19 REMARK 500 ASP B 370 35.31 -87.58 REMARK 500 LEU B 437 -62.69 66.40 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 471 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 400 SG REMARK 620 2 HEM A 471 NA 103.2 REMARK 620 3 HEM A 471 NB 94.0 89.2 REMARK 620 4 HEM A 471 NC 89.8 167.0 90.3 REMARK 620 5 HEM A 471 ND 100.3 87.7 165.7 89.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 471 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 400 SG REMARK 620 2 HEM B 471 NA 104.7 REMARK 620 3 HEM B 471 NB 93.3 90.5 REMARK 620 4 HEM B 471 NC 91.6 163.7 87.3 REMARK 620 5 HEM B 471 ND 101.6 88.2 164.8 89.7 REMARK 620 6 HOH B1254 O 171.7 81.7 81.2 81.9 83.6 REMARK 620 N 1 2 3 4 5 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 471 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 140 A 1470 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 471 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 140 B 1470 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KX4 RELATED DB: PDB REMARK 900 RELATED ID: 3KX5 RELATED DB: PDB DBREF 3KX3 A 1 470 UNP P14779 CPXB_BACME 2 471 DBREF 3KX3 B 1 470 UNP P14779 CPXB_BACME 2 471 SEQADV 3KX3 GLU A 86 UNP P14779 LEU 87 ENGINEERED MUTATION SEQADV 3KX3 GLU B 86 UNP P14779 LEU 87 ENGINEERED MUTATION SEQRES 1 A 470 THR ILE LYS GLU MET PRO GLN PRO LYS THR PHE GLY GLU SEQRES 2 A 470 LEU LYS ASN LEU PRO LEU LEU ASN THR ASP LYS PRO VAL SEQRES 3 A 470 GLN ALA LEU MET LYS ILE ALA ASP GLU LEU GLY GLU ILE SEQRES 4 A 470 PHE LYS PHE GLU ALA PRO GLY ARG VAL THR ARG TYR LEU SEQRES 5 A 470 SER SER GLN ARG LEU ILE LYS GLU ALA CYS ASP GLU SER SEQRES 6 A 470 ARG PHE ASP LYS ASN LEU SER GLN ALA LEU LYS PHE VAL SEQRES 7 A 470 ARG ASP PHE ALA GLY ASP GLY GLU PHE THR SER TRP THR SEQRES 8 A 470 HIS GLU LYS ASN TRP LYS LYS ALA HIS ASN ILE LEU LEU SEQRES 9 A 470 PRO SER PHE SER GLN GLN ALA MET LYS GLY TYR HIS ALA SEQRES 10 A 470 MET MET VAL ASP ILE ALA VAL GLN LEU VAL GLN LYS TRP SEQRES 11 A 470 GLU ARG LEU ASN ALA ASP GLU HIS ILE GLU VAL PRO GLU SEQRES 12 A 470 ASP MET THR ARG LEU THR LEU ASP THR ILE GLY LEU CYS SEQRES 13 A 470 GLY PHE ASN TYR ARG PHE ASN SER PHE TYR ARG ASP GLN SEQRES 14 A 470 PRO HIS PRO PHE ILE THR SER MET VAL ARG ALA LEU ASP SEQRES 15 A 470 GLU ALA MET ASN LYS LEU GLN ARG ALA ASN PRO ASP ASP SEQRES 16 A 470 PRO ALA TYR ASP GLU ASN LYS ARG GLN PHE GLN GLU ASP SEQRES 17 A 470 ILE LYS VAL MET ASN ASP LEU VAL ASP LYS ILE ILE ALA SEQRES 18 A 470 ASP ARG LYS ALA SER GLY GLU GLN SER ASP ASP LEU LEU SEQRES 19 A 470 THR HIS MET LEU ASN GLY LYS ASP PRO GLU THR GLY GLU SEQRES 20 A 470 PRO LEU ASP ASP GLU ASN ILE ARG TYR GLN ILE ILE THR SEQRES 21 A 470 PHE LEU ILE ALA GLY HIS GLU THR THR SER GLY LEU LEU SEQRES 22 A 470 SER PHE ALA LEU TYR PHE LEU VAL LYS ASN PRO HIS VAL SEQRES 23 A 470 LEU GLN LYS ALA ALA GLU GLU ALA ALA ARG VAL LEU VAL SEQRES 24 A 470 ASP PRO VAL PRO SER TYR LYS GLN VAL LYS GLN LEU LYS SEQRES 25 A 470 TYR VAL GLY MET VAL LEU ASN GLU ALA LEU ARG LEU TRP SEQRES 26 A 470 PRO THR ALA PRO ALA PHE SER LEU TYR ALA LYS GLU ASP SEQRES 27 A 470 THR VAL LEU GLY GLY GLU TYR PRO LEU GLU LYS GLY ASP SEQRES 28 A 470 GLU LEU MET VAL LEU ILE PRO GLN LEU HIS ARG ASP LYS SEQRES 29 A 470 THR ILE TRP GLY ASP ASP VAL GLU GLU PHE ARG PRO GLU SEQRES 30 A 470 ARG PHE GLU ASN PRO SER ALA ILE PRO GLN HIS ALA PHE SEQRES 31 A 470 LYS PRO PHE GLY ASN GLY GLN ARG ALA CYS ILE GLY GLN SEQRES 32 A 470 GLN PHE ALA LEU HIS GLU ALA THR LEU VAL LEU GLY MET SEQRES 33 A 470 MET LEU LYS HIS PHE ASP PHE GLU ASP HIS THR ASN TYR SEQRES 34 A 470 GLU LEU ASP ILE LYS GLU THR LEU THR LEU LYS PRO GLU SEQRES 35 A 470 GLY PHE VAL VAL LYS ALA LYS SER LYS LYS ILE PRO LEU SEQRES 36 A 470 GLY GLY ILE PRO SER PRO SER THR GLU GLN SER ALA LYS SEQRES 37 A 470 LYS VAL SEQRES 1 B 470 THR ILE LYS GLU MET PRO GLN PRO LYS THR PHE GLY GLU SEQRES 2 B 470 LEU LYS ASN LEU PRO LEU LEU ASN THR ASP LYS PRO VAL SEQRES 3 B 470 GLN ALA LEU MET LYS ILE ALA ASP GLU LEU GLY GLU ILE SEQRES 4 B 470 PHE LYS PHE GLU ALA PRO GLY ARG VAL THR ARG TYR LEU SEQRES 5 B 470 SER SER GLN ARG LEU ILE LYS GLU ALA CYS ASP GLU SER SEQRES 6 B 470 ARG PHE ASP LYS ASN LEU SER GLN ALA LEU LYS PHE VAL SEQRES 7 B 470 ARG ASP PHE ALA GLY ASP GLY GLU PHE THR SER TRP THR SEQRES 8 B 470 HIS GLU LYS ASN TRP LYS LYS ALA HIS ASN ILE LEU LEU SEQRES 9 B 470 PRO SER PHE SER GLN GLN ALA MET LYS GLY TYR HIS ALA SEQRES 10 B 470 MET MET VAL ASP ILE ALA VAL GLN LEU VAL GLN LYS TRP SEQRES 11 B 470 GLU ARG LEU ASN ALA ASP GLU HIS ILE GLU VAL PRO GLU SEQRES 12 B 470 ASP MET THR ARG LEU THR LEU ASP THR ILE GLY LEU CYS SEQRES 13 B 470 GLY PHE ASN TYR ARG PHE ASN SER PHE TYR ARG ASP GLN SEQRES 14 B 470 PRO HIS PRO PHE ILE THR SER MET VAL ARG ALA LEU ASP SEQRES 15 B 470 GLU ALA MET ASN LYS LEU GLN ARG ALA ASN PRO ASP ASP SEQRES 16 B 470 PRO ALA TYR ASP GLU ASN LYS ARG GLN PHE GLN GLU ASP SEQRES 17 B 470 ILE LYS VAL MET ASN ASP LEU VAL ASP LYS ILE ILE ALA SEQRES 18 B 470 ASP ARG LYS ALA SER GLY GLU GLN SER ASP ASP LEU LEU SEQRES 19 B 470 THR HIS MET LEU ASN GLY LYS ASP PRO GLU THR GLY GLU SEQRES 20 B 470 PRO LEU ASP ASP GLU ASN ILE ARG TYR GLN ILE ILE THR SEQRES 21 B 470 PHE LEU ILE ALA GLY HIS GLU THR THR SER GLY LEU LEU SEQRES 22 B 470 SER PHE ALA LEU TYR PHE LEU VAL LYS ASN PRO HIS VAL SEQRES 23 B 470 LEU GLN LYS ALA ALA GLU GLU ALA ALA ARG VAL LEU VAL SEQRES 24 B 470 ASP PRO VAL PRO SER TYR LYS GLN VAL LYS GLN LEU LYS SEQRES 25 B 470 TYR VAL GLY MET VAL LEU ASN GLU ALA LEU ARG LEU TRP SEQRES 26 B 470 PRO THR ALA PRO ALA PHE SER LEU TYR ALA LYS GLU ASP SEQRES 27 B 470 THR VAL LEU GLY GLY GLU TYR PRO LEU GLU LYS GLY ASP SEQRES 28 B 470 GLU LEU MET VAL LEU ILE PRO GLN LEU HIS ARG ASP LYS SEQRES 29 B 470 THR ILE TRP GLY ASP ASP VAL GLU GLU PHE ARG PRO GLU SEQRES 30 B 470 ARG PHE GLU ASN PRO SER ALA ILE PRO GLN HIS ALA PHE SEQRES 31 B 470 LYS PRO PHE GLY ASN GLY GLN ARG ALA CYS ILE GLY GLN SEQRES 32 B 470 GLN PHE ALA LEU HIS GLU ALA THR LEU VAL LEU GLY MET SEQRES 33 B 470 MET LEU LYS HIS PHE ASP PHE GLU ASP HIS THR ASN TYR SEQRES 34 B 470 GLU LEU ASP ILE LYS GLU THR LEU THR LEU LYS PRO GLU SEQRES 35 B 470 GLY PHE VAL VAL LYS ALA LYS SER LYS LYS ILE PRO LEU SEQRES 36 B 470 GLY GLY ILE PRO SER PRO SER THR GLU GLN SER ALA LYS SEQRES 37 B 470 LYS VAL HET HEM A 471 43 HET 140 A1470 22 HET HEM B 471 43 HET 140 B1470 22 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM 140 N-PALMITOYLGLYCINE HETSYN HEM HEME HETSYN 140 N-HEXADECANOYLGLYCINE FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 140 2(C18 H35 N O3) FORMUL 7 HOH *1231(H2 O) HELIX 1 1 PHE A 11 LYS A 15 5 5 HELIX 2 2 ASN A 16 ASN A 21 5 6 HELIX 3 3 LYS A 24 GLY A 37 1 14 HELIX 4 4 SER A 54 CYS A 62 1 9 HELIX 5 5 SER A 72 GLY A 83 1 12 HELIX 6 6 GLU A 93 LEU A 104 1 12 HELIX 7 7 PRO A 105 PHE A 107 5 3 HELIX 8 8 SER A 108 ARG A 132 1 25 HELIX 9 9 VAL A 141 ASN A 159 1 19 HELIX 10 10 ASN A 163 ARG A 167 5 5 HELIX 11 11 HIS A 171 LEU A 188 1 18 HELIX 12 12 ASP A 195 ALA A 197 5 3 HELIX 13 13 TYR A 198 ALA A 225 1 28 HELIX 14 14 ASP A 232 GLY A 240 1 9 HELIX 15 15 ASP A 250 GLY A 265 1 16 HELIX 16 16 HIS A 266 ASN A 283 1 18 HELIX 17 17 ASN A 283 LEU A 298 1 16 HELIX 18 18 SER A 304 GLN A 310 1 7 HELIX 19 19 LEU A 311 TRP A 325 1 15 HELIX 20 20 GLY A 342 GLU A 344 5 3 HELIX 21 21 ILE A 357 HIS A 361 1 5 HELIX 22 22 ASP A 363 GLY A 368 1 6 HELIX 23 23 ARG A 375 GLU A 380 5 6 HELIX 24 24 ASN A 381 ILE A 385 5 5 HELIX 25 25 ASN A 395 ALA A 399 5 5 HELIX 26 26 GLY A 402 HIS A 420 1 19 HELIX 27 27 PHE B 11 LYS B 15 5 5 HELIX 28 28 ASN B 16 ASN B 21 5 6 HELIX 29 29 LYS B 24 GLY B 37 1 14 HELIX 30 30 SER B 54 CYS B 62 1 9 HELIX 31 31 SER B 72 GLY B 83 1 12 HELIX 32 32 GLU B 93 LEU B 104 1 12 HELIX 33 33 PRO B 105 PHE B 107 5 3 HELIX 34 34 SER B 108 ARG B 132 1 25 HELIX 35 35 VAL B 141 ASN B 159 1 19 HELIX 36 36 ASN B 163 ARG B 167 5 5 HELIX 37 37 HIS B 171 LEU B 188 1 18 HELIX 38 38 ASP B 195 ALA B 197 5 3 HELIX 39 39 TYR B 198 SER B 226 1 29 HELIX 40 40 ASP B 232 GLY B 240 1 9 HELIX 41 41 ASP B 250 GLY B 265 1 16 HELIX 42 42 HIS B 266 ASN B 283 1 18 HELIX 43 43 ASN B 283 LEU B 298 1 16 HELIX 44 44 SER B 304 GLN B 310 1 7 HELIX 45 45 LEU B 311 TRP B 325 1 15 HELIX 46 46 ILE B 357 HIS B 361 1 5 HELIX 47 47 ASP B 363 GLY B 368 1 6 HELIX 48 48 ARG B 375 GLU B 380 5 6 HELIX 49 49 ASN B 381 ILE B 385 5 5 HELIX 50 50 ASN B 395 ALA B 399 5 5 HELIX 51 51 GLY B 402 HIS B 420 1 19 SHEET 1 A 5 ILE A 39 ALA A 44 0 SHEET 2 A 5 ARG A 47 LEU A 52 -1 O ARG A 47 N ALA A 44 SHEET 3 A 5 GLU A 352 LEU A 356 1 O MET A 354 N LEU A 52 SHEET 4 A 5 ALA A 330 ALA A 335 -1 N PHE A 331 O VAL A 355 SHEET 5 A 5 PHE A 67 ASN A 70 -1 N ASN A 70 O SER A 332 SHEET 1 B 3 ILE A 139 GLU A 140 0 SHEET 2 B 3 VAL A 445 SER A 450 -1 O VAL A 446 N ILE A 139 SHEET 3 B 3 PHE A 421 GLU A 424 -1 N ASP A 422 O LYS A 449 SHEET 1 C 2 THR A 339 LEU A 341 0 SHEET 2 C 2 TYR A 345 LEU A 347 -1 O LEU A 347 N THR A 339 SHEET 1 D 2 ILE A 433 GLU A 435 0 SHEET 2 D 2 LEU A 439 PRO A 441 -1 O LYS A 440 N LYS A 434 SHEET 1 E 5 ILE B 39 ALA B 44 0 SHEET 2 E 5 ARG B 47 LEU B 52 -1 O THR B 49 N PHE B 42 SHEET 3 E 5 GLU B 352 LEU B 356 1 O MET B 354 N LEU B 52 SHEET 4 E 5 ALA B 330 ALA B 335 -1 N PHE B 331 O VAL B 355 SHEET 5 E 5 PHE B 67 ASN B 70 -1 N ASN B 70 O SER B 332 SHEET 1 F 3 ILE B 139 GLU B 140 0 SHEET 2 F 3 VAL B 445 SER B 450 -1 O VAL B 446 N ILE B 139 SHEET 3 F 3 PHE B 421 GLU B 424 -1 N ASP B 422 O LYS B 449 SHEET 1 G 2 THR B 339 LEU B 341 0 SHEET 2 G 2 TYR B 345 LEU B 347 -1 O LEU B 347 N THR B 339 SHEET 1 H 2 ILE B 433 GLU B 435 0 SHEET 2 H 2 LEU B 439 PRO B 441 -1 O LYS B 440 N LYS B 434 LINK SG CYS A 400 FE HEM A 471 1555 1555 2.37 LINK SG CYS B 400 FE HEM B 471 1555 1555 2.34 LINK FE HEM B 471 O HOH B1254 1555 1555 1.92 SITE 1 AC1 28 LYS A 69 LEU A 75 GLU A 86 PHE A 87 SITE 2 AC1 28 TRP A 96 HIS A 100 PHE A 107 PHE A 261 SITE 3 AC1 28 ALA A 264 GLY A 265 THR A 268 THR A 269 SITE 4 AC1 28 PHE A 331 PRO A 392 PHE A 393 GLY A 394 SITE 5 AC1 28 ARG A 398 ALA A 399 CYS A 400 ILE A 401 SITE 6 AC1 28 ALA A 406 HOH A 477 HOH A 478 HOH A 480 SITE 7 AC1 28 HOH A 481 HOH A 510 HOH A 569 HOH A1255 SITE 1 AC2 10 LEU A 29 TYR A 51 SER A 72 GLN A 73 SITE 2 AC2 10 ALA A 74 VAL A 78 ALA A 82 LEU A 188 SITE 3 AC2 10 HOH A 660 HOH A 832 SITE 1 AC3 29 LYS B 69 GLU B 86 PHE B 87 TRP B 96 SITE 2 AC3 29 HIS B 100 PHE B 261 ALA B 264 GLY B 265 SITE 3 AC3 29 THR B 268 THR B 269 THR B 327 PHE B 331 SITE 4 AC3 29 PRO B 392 PHE B 393 GLY B 394 ARG B 398 SITE 5 AC3 29 ALA B 399 CYS B 400 ILE B 401 GLY B 402 SITE 6 AC3 29 PHE B 405 ALA B 406 HOH B 472 HOH B 483 SITE 7 AC3 29 HOH B 491 HOH B 494 HOH B 548 HOH B 618 SITE 8 AC3 29 HOH B1254 SITE 1 AC4 9 LEU B 29 ARG B 47 TYR B 51 SER B 72 SITE 2 AC4 9 GLN B 73 ALA B 74 LEU B 188 LEU B 437 SITE 3 AC4 9 HOH B 566 CRYST1 58.960 148.250 64.210 90.00 98.55 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016961 0.000000 0.002550 0.00000 SCALE2 0.000000 0.006745 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015749 0.00000