HEADER OXIDOREDUCTASE 12-APR-16 5JAB TITLE STRUCTURE OF THE BILIVERDIN REDUCTASE RV2074 FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS IN COMPLEX WITH F420 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BILIVERDIN REDUCTASE RV2074; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 STRAIN: ATCC 25618 / H37RV; SOURCE 6 GENE: RV2074, MTCY49.13; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BILIVERDIN REDUCTASE, SPLIT BETA-BARREL FOLD, FLAVIN/DEAZAFLAVIN KEYWDS 2 OXIDOREDUCTASE, F420 BINDING PROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.H.AHMED,P.D.CARR,C.J.JACKSON REVDAT 4 27-SEP-23 5JAB 1 REMARK REVDAT 3 27-SEP-17 5JAB 1 JRNL REMARK REVDAT 2 31-AUG-16 5JAB 1 JRNL REVDAT 1 13-JUL-16 5JAB 0 JRNL AUTH F.H.AHMED,A.E.MOHAMED,P.D.CARR,B.M.LEE,K.CONDIC-JURKIC, JRNL AUTH 2 M.L.O'MARA,C.J.JACKSON JRNL TITL RV2074 IS A NOVEL F420 H2 -DEPENDENT BILIVERDIN REDUCTASE IN JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS. JRNL REF PROTEIN SCI. V. 25 1692 2016 JRNL REFN ESSN 1469-896X JRNL PMID 27364382 JRNL DOI 10.1002/PRO.2975 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 62534 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3266 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4565 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 223 REMARK 3 BIN FREE R VALUE : 0.3750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4034 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 252 REMARK 3 SOLVENT ATOMS : 654 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.103 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.290 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4451 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4273 ; 0.010 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6078 ; 1.962 ; 2.021 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9756 ; 1.682 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 547 ; 7.556 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 201 ;29.052 ;21.841 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 708 ;12.345 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 64 ;18.103 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 705 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5044 ; 0.015 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1048 ; 0.008 ; 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): 2128 ; 2.014 ; 1.779 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2127 ; 2.007 ; 1.777 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2662 ; 2.924 ; 2.650 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 9 134 B 9 134 7304 0.120 0.050 REMARK 3 2 A 9 134 C 9 134 7450 0.100 0.050 REMARK 3 3 A 2 134 D 2 134 7762 0.100 0.050 REMARK 3 4 B 9 135 C 9 135 7500 0.100 0.050 REMARK 3 5 B 9 134 D 9 134 7468 0.110 0.050 REMARK 3 6 C 9 134 D 9 134 7409 0.100 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5JAB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220135. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65830 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 65.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.18100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 1.26100 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: PHASER 2.5.6 REMARK 200 STARTING MODEL: 2ASF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG3350, 0.2M MGCL2, 0.1 M REMARK 280 BISTRIS, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 292.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.31000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.31250 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.31000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.31250 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 B 1 REMARK 465 ALA B 2 REMARK 465 MET B 3 REMARK 465 VAL B 4 REMARK 465 ASN B 5 REMARK 465 THR B 6 REMARK 465 THR B 7 REMARK 465 THR B 8 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 MET C 3 REMARK 465 VAL C 4 REMARK 465 ASN C 5 REMARK 465 THR C 6 REMARK 465 THR C 7 REMARK 465 THR C 8 REMARK 465 MET D 1 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 304 O HOH A 366 1.97 REMARK 500 OE2 GLU B 121 O HOH B 301 1.98 REMARK 500 O HOH B 339 O HOH B 357 2.02 REMARK 500 O HOH C 387 O HOH C 429 2.03 REMARK 500 O HOH B 407 O HOH B 432 2.04 REMARK 500 NH1 ARG A 87 O HOH A 301 2.07 REMARK 500 O HOH C 324 O HOH C 373 2.09 REMARK 500 OD1 ASP A 12 O HOH A 302 2.10 REMARK 500 NE ARG C 112 O HOH C 301 2.12 REMARK 500 O HOH A 326 O HOH A 463 2.12 REMARK 500 O HOH A 356 O HOH A 463 2.13 REMARK 500 NH1 ARG C 9 O HOH C 302 2.15 REMARK 500 NH1 ARG B 126 O HOH B 302 2.16 REMARK 500 O HOH A 450 O HOH C 443 2.17 REMARK 500 O HOH B 336 O HOH B 359 2.18 REMARK 500 O HOH B 378 O HOH B 447 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 463 O HOH B 457 4694 2.13 REMARK 500 O HOH B 427 O HOH D 386 25105 2.17 REMARK 500 O HOH B 361 O HOH D 351 25105 2.18 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 95 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 98 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A 135 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG B 67 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 98 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP B 99 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG C 30 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG C 52 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG C 87 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP C 93 CB - CG - OD1 ANGL. DEV. = 5.8 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 TYR A 108 -101.56 -114.85 REMARK 500 TYR B 108 -99.59 -113.65 REMARK 500 TYR C 108 -96.80 -111.77 REMARK 500 GLU D 20 151.46 -48.61 REMARK 500 TYR D 108 -100.29 -113.99 REMARK 500 LEU D 134 -51.92 -120.17 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 LEU A 134 ASP A 135 -126.10 REMARK 500 LEU A 134 ASP A 135 -127.56 REMARK 500 LEU D 134 ASP D 135 -133.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: COENZYME F420-3 REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 6J4 A 201 REMARK 630 6J4 B 201 REMARK 630 6J4 C 201 REMARK 630 6J4 D 201 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: 6J2 GGL GGL GLU REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6J4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6J4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6J4 C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6J4 D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL D 202 DBREF 5JAB A 1 135 UNP P9WLL7 Y2074_MYCTU 1 135 DBREF 5JAB B 1 135 UNP P9WLL7 Y2074_MYCTU 1 135 DBREF 5JAB C 1 135 UNP P9WLL7 Y2074_MYCTU 1 135 DBREF 5JAB D 1 135 UNP P9WLL7 Y2074_MYCTU 1 135 SEQRES 1 A 135 MET ALA MET VAL ASN THR THR THR ARG LEU SER ASP ASP SEQRES 2 A 135 ALA LEU ALA PHE LEU SER GLU ARG HIS LEU ALA MET LEU SEQRES 3 A 135 THR THR LEU ARG ALA ASP ASN SER PRO HIS VAL VAL ALA SEQRES 4 A 135 VAL GLY PHE THR PHE ASP PRO LYS THR HIS ILE ALA ARG SEQRES 5 A 135 VAL ILE THR THR GLY GLY SER GLN LYS ALA VAL ASN ALA SEQRES 6 A 135 ASP ARG SER GLY LEU ALA VAL LEU SER GLN VAL ASP GLY SEQRES 7 A 135 ALA ARG TRP LEU SER LEU GLU GLY ARG ALA ALA VAL ASN SEQRES 8 A 135 SER ASP ILE ASP ALA VAL ARG ASP ALA GLU LEU ARG TYR SEQRES 9 A 135 ALA GLN ARG TYR ARG THR PRO ARG PRO ASN PRO ARG ARG SEQRES 10 A 135 VAL VAL ILE GLU VAL GLN ILE GLU ARG VAL LEU GLY SER SEQRES 11 A 135 ALA ASP LEU LEU ASP SEQRES 1 B 135 MET ALA MET VAL ASN THR THR THR ARG LEU SER ASP ASP SEQRES 2 B 135 ALA LEU ALA PHE LEU SER GLU ARG HIS LEU ALA MET LEU SEQRES 3 B 135 THR THR LEU ARG ALA ASP ASN SER PRO HIS VAL VAL ALA SEQRES 4 B 135 VAL GLY PHE THR PHE ASP PRO LYS THR HIS ILE ALA ARG SEQRES 5 B 135 VAL ILE THR THR GLY GLY SER GLN LYS ALA VAL ASN ALA SEQRES 6 B 135 ASP ARG SER GLY LEU ALA VAL LEU SER GLN VAL ASP GLY SEQRES 7 B 135 ALA ARG TRP LEU SER LEU GLU GLY ARG ALA ALA VAL ASN SEQRES 8 B 135 SER ASP ILE ASP ALA VAL ARG ASP ALA GLU LEU ARG TYR SEQRES 9 B 135 ALA GLN ARG TYR ARG THR PRO ARG PRO ASN PRO ARG ARG SEQRES 10 B 135 VAL VAL ILE GLU VAL GLN ILE GLU ARG VAL LEU GLY SER SEQRES 11 B 135 ALA ASP LEU LEU ASP SEQRES 1 C 135 MET ALA MET VAL ASN THR THR THR ARG LEU SER ASP ASP SEQRES 2 C 135 ALA LEU ALA PHE LEU SER GLU ARG HIS LEU ALA MET LEU SEQRES 3 C 135 THR THR LEU ARG ALA ASP ASN SER PRO HIS VAL VAL ALA SEQRES 4 C 135 VAL GLY PHE THR PHE ASP PRO LYS THR HIS ILE ALA ARG SEQRES 5 C 135 VAL ILE THR THR GLY GLY SER GLN LYS ALA VAL ASN ALA SEQRES 6 C 135 ASP ARG SER GLY LEU ALA VAL LEU SER GLN VAL ASP GLY SEQRES 7 C 135 ALA ARG TRP LEU SER LEU GLU GLY ARG ALA ALA VAL ASN SEQRES 8 C 135 SER ASP ILE ASP ALA VAL ARG ASP ALA GLU LEU ARG TYR SEQRES 9 C 135 ALA GLN ARG TYR ARG THR PRO ARG PRO ASN PRO ARG ARG SEQRES 10 C 135 VAL VAL ILE GLU VAL GLN ILE GLU ARG VAL LEU GLY SER SEQRES 11 C 135 ALA ASP LEU LEU ASP SEQRES 1 D 135 MET ALA MET VAL ASN THR THR THR ARG LEU SER ASP ASP SEQRES 2 D 135 ALA LEU ALA PHE LEU SER GLU ARG HIS LEU ALA MET LEU SEQRES 3 D 135 THR THR LEU ARG ALA ASP ASN SER PRO HIS VAL VAL ALA SEQRES 4 D 135 VAL GLY PHE THR PHE ASP PRO LYS THR HIS ILE ALA ARG SEQRES 5 D 135 VAL ILE THR THR GLY GLY SER GLN LYS ALA VAL ASN ALA SEQRES 6 D 135 ASP ARG SER GLY LEU ALA VAL LEU SER GLN VAL ASP GLY SEQRES 7 D 135 ALA ARG TRP LEU SER LEU GLU GLY ARG ALA ALA VAL ASN SEQRES 8 D 135 SER ASP ILE ASP ALA VAL ARG ASP ALA GLU LEU ARG TYR SEQRES 9 D 135 ALA GLN ARG TYR ARG THR PRO ARG PRO ASN PRO ARG ARG SEQRES 10 D 135 VAL VAL ILE GLU VAL GLN ILE GLU ARG VAL LEU GLY SER SEQRES 11 D 135 ALA ASP LEU LEU ASP HET 6J4 A 201 62 HET CL A 202 1 HET 6J4 B 201 62 HET CL B 202 1 HET 6J4 C 201 62 HET CL C 202 1 HET 6J4 D 201 62 HET CL D 202 1 HETNAM 6J4 COENZYME F420-3 HETNAM CL CHLORIDE ION FORMUL 5 6J4 4(C34 H43 N6 O21 P) FORMUL 6 CL 4(CL 1-) FORMUL 13 HOH *654(H2 O) HELIX 1 AA1 SER A 11 GLU A 20 1 10 HELIX 2 AA2 SER A 59 GLY A 69 1 11 HELIX 3 AA3 ASP A 93 TYR A 108 1 16 HELIX 4 AA4 ALA A 131 LEU A 134 5 4 HELIX 5 AA5 SER B 11 GLU B 20 1 10 HELIX 6 AA6 SER B 59 GLY B 69 1 11 HELIX 7 AA7 ASP B 93 TYR B 108 1 16 HELIX 8 AA8 ALA B 131 LEU B 134 5 4 HELIX 9 AA9 SER C 11 GLU C 20 1 10 HELIX 10 AB1 SER C 59 GLY C 69 1 11 HELIX 11 AB2 ASP C 93 TYR C 108 1 16 HELIX 12 AB3 ALA C 131 LEU C 134 5 4 HELIX 13 AB4 SER D 11 GLU D 20 1 10 HELIX 14 AB5 SER D 59 GLY D 69 1 11 HELIX 15 AB6 ASP D 93 TYR D 108 1 16 HELIX 16 AB7 SER D 130 ASP D 135 1 6 SHEET 1 AA1 6 ALA A 2 MET A 3 0 SHEET 2 AA1 6 ARG A 117 GLY A 129 -1 O VAL A 127 N ALA A 2 SHEET 3 AA1 6 ARG A 80 ASN A 91 -1 N ASN A 91 O VAL A 119 SHEET 4 AA1 6 LEU A 70 ASP A 77 -1 N LEU A 73 O LEU A 84 SHEET 5 AA1 6 ALA A 24 LEU A 29 -1 N THR A 27 O VAL A 72 SHEET 6 AA1 6 PRO A 35 VAL A 40 -1 O HIS A 36 N THR A 28 SHEET 1 AA2 4 ALA A 2 MET A 3 0 SHEET 2 AA2 4 ARG A 117 GLY A 129 -1 O VAL A 127 N ALA A 2 SHEET 3 AA2 4 ILE A 50 THR A 56 -1 N VAL A 53 O ILE A 120 SHEET 4 AA2 4 THR A 43 ASP A 45 -1 N ASP A 45 O ILE A 50 SHEET 1 AA3 7 PRO B 35 VAL B 40 0 SHEET 2 AA3 7 ALA B 24 LEU B 29 -1 N THR B 28 O HIS B 36 SHEET 3 AA3 7 LEU B 70 ASP B 77 -1 O VAL B 72 N THR B 27 SHEET 4 AA3 7 ARG B 80 ASN B 91 -1 O ARG B 80 N ASP B 77 SHEET 5 AA3 7 ARG B 117 GLY B 129 -1 O VAL B 119 N ASN B 91 SHEET 6 AA3 7 ILE B 50 THR B 56 -1 N VAL B 53 O ILE B 120 SHEET 7 AA3 7 THR B 43 ASP B 45 -1 N THR B 43 O ARG B 52 SHEET 1 AA4 7 PRO C 35 VAL C 40 0 SHEET 2 AA4 7 ALA C 24 LEU C 29 -1 N LEU C 26 O VAL C 38 SHEET 3 AA4 7 LEU C 70 ASP C 77 -1 O SER C 74 N MET C 25 SHEET 4 AA4 7 ARG C 80 ASN C 91 -1 O ARG C 80 N ASP C 77 SHEET 5 AA4 7 ARG C 117 GLY C 129 -1 O VAL C 119 N ASN C 91 SHEET 6 AA4 7 ILE C 50 THR C 56 -1 N VAL C 53 O ILE C 120 SHEET 7 AA4 7 THR C 43 ASP C 45 -1 N THR C 43 O ARG C 52 SHEET 1 AA5 7 PRO D 35 VAL D 40 0 SHEET 2 AA5 7 ALA D 24 LEU D 29 -1 N THR D 28 O HIS D 36 SHEET 3 AA5 7 LEU D 70 ASP D 77 -1 O VAL D 72 N THR D 27 SHEET 4 AA5 7 ARG D 80 ASN D 91 -1 O ARG D 80 N ASP D 77 SHEET 5 AA5 7 ARG D 117 GLY D 129 -1 O GLU D 121 N ALA D 89 SHEET 6 AA5 7 ILE D 50 THR D 56 -1 N VAL D 53 O ILE D 120 SHEET 7 AA5 7 THR D 43 ASP D 45 -1 N THR D 43 O ARG D 52 SITE 1 AC1 28 HIS A 36 VAL A 38 ALA A 39 VAL A 40 SITE 2 AC1 28 GLY A 41 ILE A 54 THR A 55 GLY A 58 SITE 3 AC1 28 GLN A 60 LYS A 61 ARG A 67 HOH A 327 SITE 4 AC1 28 HOH A 330 HOH A 332 HOH A 342 HOH A 351 SITE 5 AC1 28 HOH A 358 HOH A 368 HOH A 391 HOH A 406 SITE 6 AC1 28 HOH A 408 HOH A 415 HOH A 417 ARG B 9 SITE 7 AC1 28 GLY B 78 ALA B 79 TRP B 81 ARG B 126 SITE 1 AC2 3 THR A 55 ASN A 114 ARG A 117 SITE 1 AC3 26 MET A 1 GLY A 78 ALA A 79 TRP A 81 SITE 2 AC3 26 HIS B 36 VAL B 38 ALA B 39 VAL B 40 SITE 3 AC3 26 GLY B 41 ILE B 54 THR B 55 GLY B 58 SITE 4 AC3 26 GLN B 60 LYS B 61 ARG B 67 HOH B 306 SITE 5 AC3 26 HOH B 310 HOH B 317 HOH B 322 HOH B 324 SITE 6 AC3 26 HOH B 329 HOH B 330 HOH B 362 HOH B 364 SITE 7 AC3 26 HOH B 383 HOH B 392 SITE 1 AC4 4 THR B 55 ASN B 114 ARG B 117 HOH B 352 SITE 1 AC5 29 HIS C 36 VAL C 38 ALA C 39 VAL C 40 SITE 2 AC5 29 GLY C 41 ILE C 54 THR C 55 GLY C 58 SITE 3 AC5 29 SER C 59 GLN C 60 LYS C 61 ARG C 67 SITE 4 AC5 29 HOH C 326 HOH C 330 HOH C 343 HOH C 349 SITE 5 AC5 29 HOH C 351 HOH C 360 HOH C 363 HOH C 366 SITE 6 AC5 29 HOH C 370 HOH C 378 HOH C 381 HOH C 401 SITE 7 AC5 29 GLY D 78 ALA D 79 TRP D 81 ARG D 126 SITE 8 AC5 29 LEU D 128 SITE 1 AC6 3 THR C 55 ASN C 114 ARG C 117 SITE 1 AC7 29 GLY C 78 ALA C 79 TRP C 81 ARG C 126 SITE 2 AC7 29 LEU C 128 HIS D 36 VAL D 38 ALA D 39 SITE 3 AC7 29 VAL D 40 GLY D 41 ILE D 54 THR D 55 SITE 4 AC7 29 GLY D 58 GLN D 60 LYS D 61 ARG D 67 SITE 5 AC7 29 HOH D 305 HOH D 313 HOH D 319 HOH D 320 SITE 6 AC7 29 HOH D 322 HOH D 328 HOH D 330 HOH D 354 SITE 7 AC7 29 HOH D 365 HOH D 366 HOH D 370 HOH D 379 SITE 8 AC7 29 HOH D 388 SITE 1 AC8 3 THR D 55 ASN D 114 ARG D 117 CRYST1 61.756 88.620 98.625 90.00 90.00 90.00 P 2 21 21 16 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 0.016193 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011284 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010139 0.00000