HEADER OXIDOREDUCTASE 09-AUG-17 5OPA TITLE THE CRYSTAL STRUCTURE OF P450 CYP121 IN COMPLEX WITH LEAD COMPOUND 7B COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYCOCYCLOSIN SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME P450 121,CYTOCHROME P450 MT2; COMPND 5 EC: 1.14.21.9; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN CDC 1551 / SOURCE 3 OSHKOSH); SOURCE 4 ORGANISM_TAXID: 83331; SOURCE 5 GENE: CYP121, MT2336; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS CYTOCHROME P450 INHIBITOR COMPLEX, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.W.LEVY REVDAT 2 01-MAY-24 5OPA 1 REMARK REVDAT 1 28-MAR-18 5OPA 0 JRNL AUTH I.M.TABAN,H.E.A.E.ELSHIHAWY,B.TORUN,B.ZUCCHINI, JRNL AUTH 2 C.J.WILLIAMSON,D.ALTUWAIRIGI,A.S.T.NGU,K.J.MCLEAN,C.W.LEVY, JRNL AUTH 3 S.SOOD,L.B.MARINO,A.W.MUNRO,L.P.S.DE CARVALHO,C.SIMONS JRNL TITL NOVEL ARYL SUBSTITUTED PYRAZOLES AS SMALL MOLECULE JRNL TITL 2 INHIBITORS OF CYTOCHROME P450 CYP121A1: SYNTHESIS AND JRNL TITL 3 ANTIMYCOBACTERIAL EVALUATION. JRNL REF J. MED. CHEM. V. 60 10257 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 29185746 JRNL DOI 10.1021/ACS.JMEDCHEM.7B01562 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12RC1_2807: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 105317 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 5301 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 60.1029 - 4.1785 1.00 3755 205 0.1640 0.2189 REMARK 3 2 4.1785 - 3.3166 1.00 3498 201 0.1414 0.1473 REMARK 3 3 3.3166 - 2.8974 1.00 3449 184 0.1443 0.1413 REMARK 3 4 2.8974 - 2.6325 1.00 3422 190 0.1376 0.1682 REMARK 3 5 2.6325 - 2.4438 1.00 3371 185 0.1248 0.1371 REMARK 3 6 2.4438 - 2.2997 1.00 3400 182 0.1158 0.1426 REMARK 3 7 2.2997 - 2.1845 1.00 3358 186 0.1150 0.1354 REMARK 3 8 2.1845 - 2.0894 1.00 3363 188 0.1160 0.1312 REMARK 3 9 2.0894 - 2.0090 1.00 3344 178 0.1161 0.1600 REMARK 3 10 2.0090 - 1.9397 1.00 3345 174 0.1228 0.1622 REMARK 3 11 1.9397 - 1.8790 1.00 3326 190 0.1180 0.1392 REMARK 3 12 1.8790 - 1.8253 1.00 3319 172 0.1160 0.1616 REMARK 3 13 1.8253 - 1.7773 1.00 3321 177 0.1123 0.1442 REMARK 3 14 1.7773 - 1.7339 1.00 3301 196 0.1139 0.1406 REMARK 3 15 1.7339 - 1.6945 1.00 3347 155 0.1108 0.1427 REMARK 3 16 1.6945 - 1.6584 1.00 3331 168 0.1038 0.1340 REMARK 3 17 1.6584 - 1.6252 1.00 3278 178 0.1022 0.1285 REMARK 3 18 1.6252 - 1.5946 1.00 3343 169 0.1036 0.1444 REMARK 3 19 1.5946 - 1.5661 1.00 3306 181 0.1011 0.1338 REMARK 3 20 1.5661 - 1.5395 1.00 3320 155 0.0973 0.1339 REMARK 3 21 1.5395 - 1.5147 1.00 3282 183 0.0971 0.1370 REMARK 3 22 1.5147 - 1.4914 1.00 3318 171 0.1052 0.1511 REMARK 3 23 1.4914 - 1.4695 1.00 3244 179 0.1077 0.1698 REMARK 3 24 1.4695 - 1.4488 1.00 3313 174 0.1173 0.1684 REMARK 3 25 1.4488 - 1.4292 1.00 3325 167 0.1302 0.1603 REMARK 3 26 1.4292 - 1.4106 1.00 3251 172 0.1423 0.2016 REMARK 3 27 1.4106 - 1.3930 0.99 3259 164 0.1593 0.2219 REMARK 3 28 1.3930 - 1.3762 0.98 3263 148 0.1805 0.2441 REMARK 3 29 1.3762 - 1.3602 0.96 3180 156 0.2027 0.2317 REMARK 3 30 1.3602 - 1.3449 0.94 3084 173 0.2107 0.2272 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.880 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 : 0.020 3404 REMARK 3 ANGLE : 1.764 4674 REMARK 3 CHIRALITY : 0.108 513 REMARK 3 PLANARITY : 0.012 609 REMARK 3 DIHEDRAL : 17.357 1276 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 5OPA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006162. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 105311 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.345 REMARK 200 RESOLUTION RANGE LOW (A) : 53.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 15.70 REMARK 200 R MERGE (I) : 0.06770 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.50360 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.440 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: IN HOUSE MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 800 NL DROPS WITH PROTEIN-TO-MOTHER REMARK 280 LIQUOR AT A RATIO OF 1:1, BY VAPOR DIFFUSION IN 1.5 TO 2.1 M REMARK 280 AMMONIUM SULFATE AND 0.1 M SODIUM MES OR CACODYLATE FROM PH 5.5 REMARK 280 TO 6.15, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 175.69800 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 87.84900 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 131.77350 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 43.92450 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 219.62250 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 175.69800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 87.84900 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 43.92450 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 131.77350 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 219.62250 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -104.0 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 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 875 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 908 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 920 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 995 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1067 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 THR A 2 REMARK 465 ALA A 3 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 NH1 ARG A 383 O HOH A 501 1.50 REMARK 500 O HOH A 554 O HOH A 563 1.89 REMARK 500 O HOH A 563 O HOH A 789 1.95 REMARK 500 O HOH A 1015 O HOH A 1068 1.96 REMARK 500 O HOH A 524 O HOH A 651 2.06 REMARK 500 O4 SO4 A 402 O HOH A 505 2.12 REMARK 500 OE2 GLU A 194 O HOH A 506 2.15 REMARK 500 OE2 GLU A 326 O HOH A 507 2.17 REMARK 500 O HOH A 626 O HOH A 816 2.18 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 516 O HOH A 516 10665 1.75 REMARK 500 O HOH A 907 O HOH A 934 8565 2.04 REMARK 500 O HOH A 542 O HOH A 956 8565 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 LYS A 33 CE LYS A 33 NZ 0.159 REMARK 500 GLU A 81 CD GLU A 81 OE1 0.079 REMARK 500 GLU A 81 CD GLU A 81 OE2 0.080 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 32 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 32 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 LYS A 33 CD - CE - NZ ANGL. DEV. = 20.0 DEGREES REMARK 500 ARG A 134 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 134 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 383 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 383 NE - CZ - NH1 ANGL. DEV. = -3.1 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 GLU A 29 76.49 -155.48 REMARK 500 GLU A 29 76.95 -154.27 REMARK 500 PHE A 137 -73.66 -143.99 REMARK 500 ARG A 252 75.90 -117.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 72 0.10 SIDE CHAIN 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 A1070 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A1071 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A1072 DISTANCE = 6.27 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 404 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 345 SG REMARK 620 2 HEM A 404 NA 99.5 REMARK 620 3 HEM A 404 NB 92.3 88.7 REMARK 620 4 HEM A 404 NC 84.1 176.4 91.4 REMARK 620 5 HEM A 404 ND 98.3 90.0 169.3 89.3 REMARK 620 6 HOH A 546 O 173.8 86.4 85.9 90.0 83.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 404 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 345 SG REMARK 620 2 HEM A 404 NA 99.0 REMARK 620 3 HEM A 404 NB 92.4 88.4 REMARK 620 4 HEM A 404 NC 84.4 176.6 91.9 REMARK 620 5 HEM A 404 ND 98.2 89.5 169.4 89.6 REMARK 620 6 HOH A 546 O 174.6 86.1 86.1 90.5 83.4 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 SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue A2W A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 408 DBREF 5OPA A 1 396 UNP P9WPP6 CP121_MYCTO 1 396 SEQRES 1 A 396 MET THR ALA THR VAL LEU LEU GLU VAL PRO PHE SER ALA SEQRES 2 A 396 ARG GLY ASP ARG ILE PRO ASP ALA VAL ALA GLU LEU ARG SEQRES 3 A 396 THR ARG GLU PRO ILE ARG LYS VAL ARG THR ILE THR GLY SEQRES 4 A 396 ALA GLU ALA TRP LEU VAL SER SER TYR ALA LEU CYS THR SEQRES 5 A 396 GLN VAL LEU GLU ASP ARG ARG PHE SER MET LYS GLU THR SEQRES 6 A 396 ALA ALA ALA GLY ALA PRO ARG LEU ASN ALA LEU THR VAL SEQRES 7 A 396 PRO PRO GLU VAL VAL ASN ASN MET GLY ASN ILE ALA ASP SEQRES 8 A 396 ALA GLY LEU ARG LYS ALA VAL MET LYS ALA ILE THR PRO SEQRES 9 A 396 LYS ALA PRO GLY LEU GLU GLN PHE LEU ARG ASP THR ALA SEQRES 10 A 396 ASN SER LEU LEU ASP ASN LEU ILE THR GLU GLY ALA PRO SEQRES 11 A 396 ALA ASP LEU ARG ASN ASP PHE ALA ASP PRO LEU ALA THR SEQRES 12 A 396 ALA LEU HIS CYS LYS VAL LEU GLY ILE PRO GLN GLU ASP SEQRES 13 A 396 GLY PRO LYS LEU PHE ARG SER LEU SER ILE ALA PHE MET SEQRES 14 A 396 SER SER ALA ASP PRO ILE PRO ALA ALA LYS ILE ASN TRP SEQRES 15 A 396 ASP ARG ASP ILE GLU TYR MET ALA GLY ILE LEU GLU ASN SEQRES 16 A 396 PRO ASN ILE THR THR GLY LEU MET GLY GLU LEU SER ARG SEQRES 17 A 396 LEU ARG LYS ASP PRO ALA TYR SER HIS VAL SER ASP GLU SEQRES 18 A 396 LEU PHE ALA THR ILE GLY VAL THR PHE PHE GLY ALA GLY SEQRES 19 A 396 VAL ILE SER THR GLY SER PHE LEU THR THR ALA LEU ILE SEQRES 20 A 396 SER LEU ILE GLN ARG PRO GLN LEU ARG ASN LEU LEU HIS SEQRES 21 A 396 GLU LYS PRO GLU LEU ILE PRO ALA GLY VAL GLU GLU LEU SEQRES 22 A 396 LEU ARG ILE ASN LEU SER PHE ALA ASP GLY LEU PRO ARG SEQRES 23 A 396 LEU ALA THR ALA ASP ILE GLN VAL GLY ASP VAL LEU VAL SEQRES 24 A 396 ARG LYS GLY GLU LEU VAL LEU VAL LEU LEU GLU GLY ALA SEQRES 25 A 396 ASN PHE ASP PRO GLU HIS PHE PRO ASN PRO GLY SER ILE SEQRES 26 A 396 GLU LEU ASP ARG PRO ASN PRO THR SER HIS LEU ALA PHE SEQRES 27 A 396 GLY ARG GLY GLN HIS PHE CYS PRO GLY SER ALA LEU GLY SEQRES 28 A 396 ARG ARG HIS ALA GLN ILE GLY ILE GLU ALA LEU LEU LYS SEQRES 29 A 396 LYS MET PRO GLY VAL ASP LEU ALA VAL PRO ILE ASP GLN SEQRES 30 A 396 LEU VAL TRP ARG THR ARG PHE GLN ARG ARG ILE PRO GLU SEQRES 31 A 396 ARG LEU PRO VAL LEU TRP HET SO4 A 401 5 HET SO4 A 402 5 HET SO4 A 403 5 HET HEM A 404 86 HET A2W A 405 24 HET SO4 A 406 5 HET SO4 A 407 5 HET PEG A 408 7 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM A2W 3-(4-FLUOROPHENYL)-4-(IMIDAZOL-1-YLMETHYL)-1-PHENYL- HETNAM 2 A2W PYRAZOLE HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN HEM HEME FORMUL 2 SO4 5(O4 S 2-) FORMUL 5 HEM C34 H32 FE N4 O4 FORMUL 6 A2W C19 H15 F N4 FORMUL 9 PEG C4 H10 O3 FORMUL 10 HOH *572(H2 O) HELIX 1 AA1 ASP A 20 GLU A 29 1 10 HELIX 2 AA2 SER A 47 ASP A 57 1 11 HELIX 3 AA3 MET A 62 ALA A 67 5 6 HELIX 4 AA4 PRO A 79 VAL A 83 5 5 HELIX 5 AA5 ASN A 84 ALA A 92 1 9 HELIX 6 AA6 LEU A 94 ILE A 102 1 9 HELIX 7 AA7 GLY A 108 GLY A 128 1 21 HELIX 8 AA8 PHE A 137 GLY A 151 1 15 HELIX 9 AA9 PRO A 153 GLU A 155 5 3 HELIX 10 AB1 ASP A 156 SER A 163 1 8 HELIX 11 AB2 SER A 163 PHE A 168 1 6 HELIX 12 AB3 ILE A 175 ASN A 195 1 21 HELIX 13 AB4 THR A 200 LYS A 211 1 12 HELIX 14 AB5 ASP A 212 SER A 216 5 5 HELIX 15 AB6 SER A 219 GLN A 251 1 33 HELIX 16 AB7 ARG A 252 LYS A 262 1 11 HELIX 17 AB8 LEU A 265 ILE A 276 1 12 HELIX 18 AB9 LEU A 308 PHE A 314 1 7 HELIX 19 AC1 ARG A 340 PHE A 344 5 5 HELIX 20 AC2 GLY A 347 MET A 366 1 20 HELIX 21 AC3 PRO A 374 LEU A 378 5 5 SHEET 1 AA1 5 ILE A 31 ARG A 35 0 SHEET 2 AA1 5 GLU A 41 VAL A 45 -1 O LEU A 44 N ARG A 32 SHEET 3 AA1 5 LEU A 304 VAL A 307 1 O LEU A 306 N TRP A 43 SHEET 4 AA1 5 LEU A 284 ALA A 288 -1 N ARG A 286 O VAL A 305 SHEET 5 AA1 5 PHE A 60 SER A 61 -1 N SER A 61 O LEU A 287 SHEET 1 AA2 3 ALA A 131 ASP A 132 0 SHEET 2 AA2 3 PRO A 393 LEU A 395 -1 O VAL A 394 N ALA A 131 SHEET 3 AA2 3 ASP A 370 LEU A 371 -1 N ASP A 370 O LEU A 395 SHEET 1 AA3 2 ILE A 292 VAL A 294 0 SHEET 2 AA3 2 VAL A 297 VAL A 299 -1 O VAL A 297 N VAL A 294 LINK SG CYS A 345 FE AHEM A 404 1555 1555 2.28 LINK SG CYS A 345 FE BHEM A 404 1555 1555 2.28 LINK FE AHEM A 404 O HOH A 546 1555 1555 2.23 LINK FE BHEM A 404 O HOH A 546 1555 1555 2.23 CISPEP 1 VAL A 9 PRO A 10 0 2.45 CISPEP 2 ALA A 129 PRO A 130 0 0.10 SITE 1 AC1 8 LYS A 211 PRO A 330 ASN A 331 PRO A 332 SITE 2 AC1 8 THR A 333 SER A 334 HOH A 523 HOH A 704 SITE 1 AC2 5 SER A 12 ARG A 17 HOH A 505 HOH A 539 SITE 2 AC2 5 HOH A 608 SITE 1 AC3 8 ARG A 58 SER A 61 MET A 62 LYS A 63 SITE 2 AC3 8 HIS A 343 HOH A 556 HOH A 559 HOH A 703 SITE 1 AC4 29 MET A 62 MET A 86 HIS A 146 PHE A 230 SITE 2 AC4 29 ALA A 233 GLY A 234 SER A 237 THR A 238 SITE 3 AC4 29 PHE A 241 PHE A 280 LEU A 284 ARG A 286 SITE 4 AC4 29 ALA A 337 PHE A 338 GLY A 339 HIS A 343 SITE 5 AC4 29 CYS A 345 PRO A 346 GLY A 347 GLY A 351 SITE 6 AC4 29 A2W A 405 SO4 A 407 HOH A 521 HOH A 530 SITE 7 AC4 29 HOH A 534 HOH A 546 HOH A 593 HOH A 802 SITE 8 AC4 29 HOH A 866 SITE 1 AC5 17 VAL A 78 VAL A 82 ASN A 85 ALA A 167 SITE 2 AC5 17 PHE A 168 TRP A 182 VAL A 228 THR A 229 SITE 3 AC5 17 GLY A 232 GLN A 385 HEM A 404 SO4 A 407 SITE 4 AC5 17 HOH A 536 HOH A 545 HOH A 663 HOH A 768 SITE 5 AC5 17 HOH A 796 SITE 1 AC6 8 ARG A 134 ASN A 135 PHE A 161 ARG A 381 SITE 2 AC6 8 ARG A 391 HOH A 508 HOH A 528 HOH A 551 SITE 1 AC7 6 PHE A 168 ARG A 386 HEM A 404 A2W A 405 SITE 2 AC7 6 HOH A 541 HOH A 546 SITE 1 AC8 11 SER A 165 ILE A 166 MET A 169 GLN A 377 SITE 2 AC8 11 LEU A 378 ARG A 391 PRO A 393 HOH A 527 SITE 3 AC8 11 HOH A 621 HOH A 854 HOH A 860 CRYST1 77.887 77.887 263.547 90.00 90.00 120.00 P 65 2 2 12 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 0.012839 0.007413 0.000000 0.00000 SCALE2 0.000000 0.014825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003794 0.00000