HEADER OXIDOREDUCTASE 19-JAN-15 4XQ6 TITLE CRYSTAL STRUCTURE OF DIHYDROOROTATE DEHYDROGENSE FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTATE DEHYDROGENASE (QUINONE); COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 31-353; COMPND 5 SYNONYM: DHODEHASE, DHODASE, DIHYDROOROTATE OXIDASE; COMPND 6 EC: 1.3.5.2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RA; SOURCE 3 ORGANISM_TAXID: 419947; SOURCE 4 STRAIN: H37RA; SOURCE 5 GENE: PYRD, MRA_2153; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3)PLYSS AG; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS DIHYDROOROTATE DEHYDROGENSE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.KISHOR,A.ADDLAGATTA REVDAT 2 20-MAR-24 4XQ6 1 REMARK LINK REVDAT 1 20-JAN-16 4XQ6 0 JRNL AUTH C.KISHOR,A.ADDLAGATTA JRNL TITL CRYSTAL STRUCTURE OF DIHYDROOROTATE DEHYDROGENASE FORM JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 37550 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1979 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1378 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 46.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.1970 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4747 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : -0.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.202 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.179 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.257 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5025 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4913 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6863 ; 1.968 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11234 ; 0.989 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 661 ; 7.147 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 207 ;33.904 ;21.449 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 780 ;18.233 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 65 ;17.751 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 781 ; 0.145 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5754 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1149 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2590 ; 2.461 ; 2.647 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2589 ; 2.460 ; 2.646 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3245 ; 3.620 ; 3.953 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3246 ; 3.619 ; 3.954 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2435 ; 3.044 ; 3.046 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2434 ; 3.045 ; 3.046 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3611 ; 4.698 ; 4.410 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5955 ; 6.703 ;22.006 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5903 ; 6.669 ;21.974 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4XQ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000206042. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : CU REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : DENZO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39530 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 27.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22-27% PEG 3350, 0.1M BIS-TRIS PH 5.0, REMARK 280 0.2M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K 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 53.46050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 10 REMARK 465 GLY A 11 REMARK 465 SER A 12 REMARK 465 SER A 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 HIS A 19 REMARK 465 SER A 20 REMARK 465 SER A 21 REMARK 465 GLY A 22 REMARK 465 LEU A 23 REMARK 465 VAL A 24 REMARK 465 PRO A 25 REMARK 465 ARG A 26 REMARK 465 GLY A 27 REMARK 465 SER A 28 REMARK 465 HIS A 29 REMARK 465 MET A 30 REMARK 465 GLY A 98 REMARK 465 ASN A 99 REMARK 465 PRO A 100 REMARK 465 ALA A 101 REMARK 465 PRO A 102 REMARK 465 ARG A 103 REMARK 465 MET B 10 REMARK 465 GLY B 11 REMARK 465 SER B 12 REMARK 465 SER B 13 REMARK 465 HIS B 14 REMARK 465 HIS B 15 REMARK 465 HIS B 16 REMARK 465 HIS B 17 REMARK 465 HIS B 18 REMARK 465 HIS B 19 REMARK 465 SER B 20 REMARK 465 SER B 21 REMARK 465 GLY B 22 REMARK 465 LEU B 23 REMARK 465 VAL B 24 REMARK 465 PRO B 25 REMARK 465 ARG B 26 REMARK 465 GLY B 98 REMARK 465 ASN B 99 REMARK 465 PRO B 100 REMARK 465 ALA B 101 REMARK 465 PRO B 102 REMARK 465 ARG B 103 REMARK 465 ARG B 353 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 OD1 ASP A 298 NH2 ARG A 335 2.06 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 186 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ASP B 46 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 PRO B 136 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG B 303 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 PHE A 54 51.38 36.01 REMARK 500 PHE A 68 -63.74 -107.00 REMARK 500 HIS A 134 124.06 96.97 REMARK 500 ARG A 135 57.34 78.90 REMARK 500 PRO A 136 175.77 -57.88 REMARK 500 VAL A 282 13.47 -146.65 REMARK 500 TYR A 314 -59.07 -134.07 REMARK 500 ARG A 323 -55.93 -27.12 REMARK 500 GLN B 96 63.67 -151.96 REMARK 500 PRO B 136 -136.10 -14.02 REMARK 500 GLU B 137 -71.41 121.29 REMARK 500 ALA B 152 -47.69 116.86 REMARK 500 ASN B 241 -177.33 -66.64 REMARK 500 TYR B 314 -60.17 -127.13 REMARK 500 ARG B 323 -63.39 -91.37 REMARK 500 TRP B 324 -56.57 -8.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 134 ARG A 135 32.49 REMARK 500 ASP B 338 GLY B 339 54.76 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 MG B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 513 O REMARK 620 2 HOH A 521 O 94.7 REMARK 620 3 ASP B 227 OD2 83.4 171.0 REMARK 620 4 HOH B 506 O 179.2 85.2 96.6 REMARK 620 5 HOH B 528 O 84.6 94.1 94.5 96.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMN B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 405 DBREF 4XQ6 A 31 353 UNP A5U4G5 PYRD_MYCTA 31 353 DBREF 4XQ6 B 31 353 UNP A5U4G5 PYRD_MYCTA 31 353 SEQADV 4XQ6 MET A 10 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 GLY A 11 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 SER A 12 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 SER A 13 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS A 14 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS A 15 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS A 16 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS A 17 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS A 18 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS A 19 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 SER A 20 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 SER A 21 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 GLY A 22 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 LEU A 23 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 VAL A 24 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 PRO A 25 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 ARG A 26 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 GLY A 27 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 SER A 28 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS A 29 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 MET A 30 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 MET B 10 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 GLY B 11 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 SER B 12 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 SER B 13 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS B 14 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS B 15 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS B 16 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS B 17 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS B 18 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS B 19 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 SER B 20 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 SER B 21 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 GLY B 22 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 LEU B 23 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 VAL B 24 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 PRO B 25 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 ARG B 26 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 GLY B 27 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 SER B 28 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 HIS B 29 UNP A5U4G5 EXPRESSION TAG SEQADV 4XQ6 MET B 30 UNP A5U4G5 EXPRESSION TAG SEQRES 1 A 344 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 344 LEU VAL PRO ARG GLY SER HIS MET VAL ALA PRO VAL ARG SEQRES 3 A 344 ARG LEU LEU ARG ARG LEU LEU GLY PRO THR ASP PRO VAL SEQRES 4 A 344 LEU ALA SER THR VAL PHE GLY VAL ARG PHE PRO ALA PRO SEQRES 5 A 344 LEU GLY LEU ALA ALA GLY PHE ASP LYS ASP GLY THR ALA SEQRES 6 A 344 LEU SER SER TRP GLY ALA MET GLY PHE GLY TYR ALA GLU SEQRES 7 A 344 ILE GLY THR VAL THR ALA HIS PRO GLN PRO GLY ASN PRO SEQRES 8 A 344 ALA PRO ARG LEU PHE ARG LEU ALA ASP ASP ARG ALA LEU SEQRES 9 A 344 LEU ASN ARG MET GLY PHE ASN ASN HIS GLY ALA ARG ALA SEQRES 10 A 344 LEU ALA ILE ARG LEU ALA ARG HIS ARG PRO GLU ILE PRO SEQRES 11 A 344 ILE GLY VAL ASN ILE GLY LYS THR LYS LYS THR PRO ALA SEQRES 12 A 344 GLY ASP ALA VAL ASN ASP TYR ARG ALA SER ALA ARG MET SEQRES 13 A 344 VAL GLY PRO LEU ALA SER TYR LEU VAL VAL ASN VAL SER SEQRES 14 A 344 SER PRO ASN THR PRO GLY LEU ARG ASP LEU GLN ALA VAL SEQRES 15 A 344 GLU SER LEU ARG PRO ILE LEU SER ALA VAL ARG ALA GLU SEQRES 16 A 344 THR SER THR PRO VAL LEU VAL LYS ILE ALA PRO ASP LEU SEQRES 17 A 344 SER ASP SER ASP LEU ASP ASP ILE ALA ASP LEU ALA VAL SEQRES 18 A 344 GLU LEU ASP LEU ALA GLY ILE VAL ALA THR ASN THR THR SEQRES 19 A 344 VAL SER ARG ASP GLY LEU THR THR PRO GLY VAL ASP ARG SEQRES 20 A 344 LEU GLY PRO GLY GLY ILE SER GLY PRO PRO LEU ALA GLN SEQRES 21 A 344 ARG ALA VAL GLN VAL LEU ARG ARG LEU TYR ASP ARG VAL SEQRES 22 A 344 GLY ASP ARG LEU ALA LEU ILE SER VAL GLY GLY ILE GLU SEQRES 23 A 344 THR ALA ASP ASP ALA TRP GLU ARG ILE THR ALA GLY ALA SEQRES 24 A 344 SER LEU LEU GLN GLY TYR THR GLY PHE ILE TYR GLY GLY SEQRES 25 A 344 GLU ARG TRP ALA LYS ASP ILE HIS GLU GLY ILE ALA ARG SEQRES 26 A 344 ARG LEU HIS ASP GLY GLY PHE GLY SER LEU HIS GLU ALA SEQRES 27 A 344 VAL GLY SER ALA ARG ARG SEQRES 1 B 344 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 344 LEU VAL PRO ARG GLY SER HIS MET VAL ALA PRO VAL ARG SEQRES 3 B 344 ARG LEU LEU ARG ARG LEU LEU GLY PRO THR ASP PRO VAL SEQRES 4 B 344 LEU ALA SER THR VAL PHE GLY VAL ARG PHE PRO ALA PRO SEQRES 5 B 344 LEU GLY LEU ALA ALA GLY PHE ASP LYS ASP GLY THR ALA SEQRES 6 B 344 LEU SER SER TRP GLY ALA MET GLY PHE GLY TYR ALA GLU SEQRES 7 B 344 ILE GLY THR VAL THR ALA HIS PRO GLN PRO GLY ASN PRO SEQRES 8 B 344 ALA PRO ARG LEU PHE ARG LEU ALA ASP ASP ARG ALA LEU SEQRES 9 B 344 LEU ASN ARG MET GLY PHE ASN ASN HIS GLY ALA ARG ALA SEQRES 10 B 344 LEU ALA ILE ARG LEU ALA ARG HIS ARG PRO GLU ILE PRO SEQRES 11 B 344 ILE GLY VAL ASN ILE GLY LYS THR LYS LYS THR PRO ALA SEQRES 12 B 344 GLY ASP ALA VAL ASN ASP TYR ARG ALA SER ALA ARG MET SEQRES 13 B 344 VAL GLY PRO LEU ALA SER TYR LEU VAL VAL ASN VAL SER SEQRES 14 B 344 SER PRO ASN THR PRO GLY LEU ARG ASP LEU GLN ALA VAL SEQRES 15 B 344 GLU SER LEU ARG PRO ILE LEU SER ALA VAL ARG ALA GLU SEQRES 16 B 344 THR SER THR PRO VAL LEU VAL LYS ILE ALA PRO ASP LEU SEQRES 17 B 344 SER ASP SER ASP LEU ASP ASP ILE ALA ASP LEU ALA VAL SEQRES 18 B 344 GLU LEU ASP LEU ALA GLY ILE VAL ALA THR ASN THR THR SEQRES 19 B 344 VAL SER ARG ASP GLY LEU THR THR PRO GLY VAL ASP ARG SEQRES 20 B 344 LEU GLY PRO GLY GLY ILE SER GLY PRO PRO LEU ALA GLN SEQRES 21 B 344 ARG ALA VAL GLN VAL LEU ARG ARG LEU TYR ASP ARG VAL SEQRES 22 B 344 GLY ASP ARG LEU ALA LEU ILE SER VAL GLY GLY ILE GLU SEQRES 23 B 344 THR ALA ASP ASP ALA TRP GLU ARG ILE THR ALA GLY ALA SEQRES 24 B 344 SER LEU LEU GLN GLY TYR THR GLY PHE ILE TYR GLY GLY SEQRES 25 B 344 GLU ARG TRP ALA LYS ASP ILE HIS GLU GLY ILE ALA ARG SEQRES 26 B 344 ARG LEU HIS ASP GLY GLY PHE GLY SER LEU HIS GLU ALA SEQRES 27 B 344 VAL GLY SER ALA ARG ARG HET FMN A 401 31 HET CL A 402 1 HET CL A 403 1 HET MG B 401 1 HET FMN B 402 31 HET CL B 403 1 HET CL B 404 1 HET CL B 405 1 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 4 CL 5(CL 1-) FORMUL 6 MG MG 2+ FORMUL 11 HOH *213(H2 O) HELIX 1 AA1 VAL A 31 GLY A 43 1 13 HELIX 2 AA2 ASP A 46 ALA A 50 5 5 HELIX 3 AA3 ALA A 74 TRP A 78 5 5 HELIX 4 AA4 ALA A 108 ARG A 111 5 4 HELIX 5 AA5 GLY A 123 ARG A 133 1 11 HELIX 6 AA6 PRO A 151 GLY A 153 5 3 HELIX 7 AA7 ASP A 154 GLY A 167 1 14 HELIX 8 AA8 GLY A 184 GLN A 189 5 6 HELIX 9 AA9 ALA A 190 THR A 205 1 16 HELIX 10 AB1 SER A 218 LEU A 232 1 15 HELIX 11 AB2 GLY A 264 PRO A 266 5 3 HELIX 12 AB3 LEU A 267 GLY A 283 1 17 HELIX 13 AB4 THR A 296 ALA A 306 1 11 HELIX 14 AB5 TYR A 314 GLY A 321 1 8 HELIX 15 AB6 GLU A 322 GLY A 339 1 18 HELIX 16 AB7 SER A 343 VAL A 348 1 6 HELIX 17 AB8 GLY A 349 ARG A 353 5 5 HELIX 18 AB9 VAL B 31 GLY B 43 1 13 HELIX 19 AC1 ASP B 46 ALA B 50 5 5 HELIX 20 AC2 ALA B 74 TRP B 78 5 5 HELIX 21 AC3 ALA B 108 ARG B 111 5 4 HELIX 22 AC4 GLY B 123 HIS B 134 1 12 HELIX 23 AC5 ASP B 154 GLY B 167 1 14 HELIX 24 AC6 LEU B 185 GLN B 189 5 5 HELIX 25 AC7 ALA B 190 THR B 205 1 16 HELIX 26 AC8 SER B 218 LEU B 232 1 15 HELIX 27 AC9 GLY B 253 LEU B 257 5 5 HELIX 28 AD1 GLY B 264 PRO B 266 5 3 HELIX 29 AD2 LEU B 267 GLY B 283 1 17 HELIX 30 AD3 THR B 296 GLY B 307 1 12 HELIX 31 AD4 TYR B 314 GLY B 321 1 8 HELIX 32 AD5 ARG B 323 GLY B 339 1 17 HELIX 33 AD6 SER B 343 VAL B 348 1 6 SHEET 1 AA1 2 SER A 51 VAL A 53 0 SHEET 2 AA1 2 VAL A 56 PHE A 58 -1 O PHE A 58 N SER A 51 SHEET 1 AA2 9 LEU A 62 LEU A 64 0 SHEET 2 AA2 9 ALA A 86 THR A 92 1 O GLU A 87 N LEU A 64 SHEET 3 AA2 9 ILE A 140 GLY A 145 1 O ASN A 143 N ILE A 88 SHEET 4 AA2 9 TYR A 172 ASN A 176 1 O ASN A 176 N ILE A 144 SHEET 5 AA2 9 VAL A 209 ILE A 213 1 O LEU A 210 N LEU A 173 SHEET 6 AA2 9 GLY A 236 ALA A 239 1 O VAL A 238 N VAL A 211 SHEET 7 AA2 9 ALA A 287 VAL A 291 1 O ILE A 289 N ILE A 237 SHEET 8 AA2 9 LEU A 310 GLY A 313 1 O LEU A 310 N SER A 290 SHEET 9 AA2 9 LEU A 62 LEU A 64 1 N GLY A 63 O LEU A 311 SHEET 1 AA3 3 PHE A 105 LEU A 107 0 SHEET 2 AA3 3 ALA A 112 ASN A 115 -1 O ALA A 112 N LEU A 107 SHEET 3 AA3 3 GLY A 261 SER A 263 -1 O GLY A 261 N ASN A 115 SHEET 1 AA4 2 SER B 51 VAL B 53 0 SHEET 2 AA4 2 VAL B 56 PHE B 58 -1 O VAL B 56 N VAL B 53 SHEET 1 AA5 9 LEU B 62 LEU B 64 0 SHEET 2 AA5 9 TYR B 85 VAL B 91 1 O GLU B 87 N LEU B 64 SHEET 3 AA5 9 ILE B 140 ILE B 144 1 O GLY B 141 N ILE B 88 SHEET 4 AA5 9 TYR B 172 ASN B 176 1 O VAL B 174 N ILE B 144 SHEET 5 AA5 9 VAL B 209 ILE B 213 1 O LEU B 210 N LEU B 173 SHEET 6 AA5 9 GLY B 236 ALA B 239 1 O VAL B 238 N VAL B 211 SHEET 7 AA5 9 ALA B 287 VAL B 291 1 O ILE B 289 N ALA B 239 SHEET 8 AA5 9 LEU B 310 GLY B 313 1 O LEU B 310 N SER B 290 SHEET 9 AA5 9 LEU B 62 LEU B 64 1 N GLY B 63 O LEU B 311 SHEET 1 AA6 3 PHE B 105 LEU B 107 0 SHEET 2 AA6 3 ALA B 112 ASN B 115 -1 O ALA B 112 N LEU B 107 SHEET 3 AA6 3 GLY B 261 SER B 263 -1 O GLY B 261 N ASN B 115 LINK O HOH A 513 MG MG B 401 1556 1555 2.16 LINK O HOH A 521 MG MG B 401 1556 1555 2.17 LINK OD2 ASP B 227 MG MG B 401 1555 1555 2.10 LINK MG MG B 401 O HOH B 506 1555 1555 2.14 LINK MG MG B 401 O HOH B 528 1555 1555 2.13 CISPEP 1 GLY A 89 THR A 90 0 -0.79 CISPEP 2 ALA A 239 THR A 240 0 25.99 CISPEP 3 GLY B 89 THR B 90 0 2.32 CISPEP 4 ALA B 239 THR B 240 0 24.92 CISPEP 5 GLY B 339 GLY B 340 0 -14.76 SITE 1 AC1 23 ALA A 65 ALA A 66 GLY A 67 THR A 90 SITE 2 AC1 23 ASN A 115 ASN A 143 ASN A 176 SER A 179 SITE 3 AC1 23 LYS A 212 THR A 240 ASN A 241 SER A 263 SITE 4 AC1 23 GLY A 264 LEU A 267 VAL A 291 GLY A 292 SITE 5 AC1 23 GLY A 293 GLY A 313 TYR A 314 THR A 315 SITE 6 AC1 23 HOH A 536 HOH A 570 HOH A 603 SITE 1 AC2 3 PHE A 119 THR A 182 HOH A 573 SITE 1 AC3 4 ASN A 115 THR A 242 GLY A 261 HOH A 601 SITE 1 AC4 6 HIS A 94 HOH A 513 HOH A 521 ASP B 227 SITE 2 AC4 6 HOH B 506 HOH B 528 SITE 1 AC5 23 ALA B 65 ALA B 66 GLY B 67 THR B 90 SITE 2 AC5 23 ASN B 115 ASN B 143 ASN B 176 LYS B 212 SITE 3 AC5 23 THR B 240 ASN B 241 SER B 263 GLY B 264 SITE 4 AC5 23 LEU B 267 VAL B 291 GLY B 292 GLY B 293 SITE 5 AC5 23 GLY B 313 TYR B 314 THR B 315 HOH B 543 SITE 6 AC5 23 HOH B 546 HOH B 595 HOH B 599 SITE 1 AC6 5 ASN B 115 PRO B 180 THR B 242 HOH B 593 SITE 2 AC6 5 HOH B 596 SITE 1 AC7 2 PHE B 119 THR B 182 SITE 1 AC8 1 ARG B 133 CRYST1 48.335 106.921 65.089 90.00 106.21 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 0.020689 0.000000 0.006013 0.00000 SCALE2 0.000000 0.009353 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015999 0.00000