HEADER OXIDOREDUCTASE 17-FEB-15 4Y9I TITLE STRUCTURE OF F420-H2 DEPENDENT REDUCTASE (FDR-A) MSMEG_2027 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYCOBACTERIUM TUBERCULOSIS PARALOGOUS FAMILY 11; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 27-140; COMPND 5 SYNONYM: NITROREDUCTASE,UNCHARACTERIZED PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 700084 / SOURCE 3 MC(2)155); SOURCE 4 ORGANISM_TAXID: 246196; SOURCE 5 STRAIN: ATCC 700084 / MC(2)155; SOURCE 6 GENE: MSMEG_2027, MSMEI_1982, LJ00_10110; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS F420, QUINONE, REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.H.AHMED,P.D.CARR,C.J.JACKSON REVDAT 4 27-SEP-23 4Y9I 1 REMARK REVDAT 3 01-NOV-17 4Y9I 1 JRNL REMARK REVDAT 2 04-NOV-15 4Y9I 1 JRNL REVDAT 1 21-OCT-15 4Y9I 0 JRNL AUTH F.H.AHMED,P.D.CARR,B.M.LEE,L.AFRIAT-JURNOU,A.E.MOHAMED, JRNL AUTH 2 N.S.HONG,J.FLANAGAN,M.C.TAYLOR,C.GREENING,C.J.JACKSON JRNL TITL SEQUENCE-STRUCTURE-FUNCTION CLASSIFICATION OF A JRNL TITL 2 CATALYTICALLY DIVERSE OXIDOREDUCTASE SUPERFAMILY IN JRNL TITL 3 MYCOBACTERIA. JRNL REF J.MOL.BIOL. V. 427 3554 2015 JRNL REFN ESSN 1089-8638 JRNL PMID 26434506 JRNL DOI 10.1016/J.JMB.2015.09.021 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 16330 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1625 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 26.1985 - 3.4273 0.94 2457 140 0.1266 0.1504 REMARK 3 2 3.4273 - 2.7212 0.97 2586 131 0.1388 0.1652 REMARK 3 3 2.7212 - 2.3775 0.98 2546 128 0.1480 0.1521 REMARK 3 4 2.3775 - 2.1603 0.98 2592 123 0.1506 0.2380 REMARK 3 5 2.1603 - 2.0055 0.97 2559 157 0.1550 0.2006 REMARK 3 6 2.0055 - 1.8873 0.97 2531 131 0.1450 0.2064 REMARK 3 7 1.8873 - 1.7928 0.96 2541 117 0.1541 0.2380 REMARK 3 8 1.7928 - 1.7148 0.96 2526 113 0.1762 0.2815 REMARK 3 9 1.7148 - 1.6488 0.95 2455 130 0.1906 0.2312 REMARK 3 10 1.6488 - 1.5919 0.94 2495 144 0.2046 0.2419 REMARK 3 11 1.5919 - 1.5421 0.94 2416 169 0.2314 0.2914 REMARK 3 12 1.5421 - 1.4980 0.92 2374 142 0.2674 0.3340 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.040 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 1013 REMARK 3 ANGLE : 1.909 1388 REMARK 3 CHIRALITY : 0.178 145 REMARK 3 PLANARITY : 0.013 184 REMARK 3 DIHEDRAL : 14.815 384 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 4Y9I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : XENOCS GENIX 3D CU HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16332 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.498 REMARK 200 RESOLUTION RANGE LOW (A) : 26.195 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.51400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3R5Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEGMME5000, 0.05 M IMIDAZOLE, PH REMARK 280 6.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 14.29268 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 38.53917 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 14.29268 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.42500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 38.53917 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 300 REMARK: MONOMER CONFIRMED BY GEL FILTRATION 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 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 357 O HOH A 367 1.58 REMARK 500 O HOH A 352 O HOH A 441 1.86 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 304 O HOH A 327 4557 2.13 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 GLU A 140 CD GLU A 140 OE1 -0.077 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 99 NE - CZ - NH2 ANGL. DEV. = -3.4 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 68 52.53 -144.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 201 DBREF 4Y9I A 27 140 UNP A0QU01 A0QU01_MYCS2 27 140 SEQRES 1 A 114 GLY VAL HIS VAL LEU ASP ARG PRO ILE VAL LEU PHE THR SEQRES 2 A 114 THR THR GLY ALA LYS SER GLY LYS LYS ARG TYR VAL PRO SEQRES 3 A 114 LEU MET ARG VAL GLU GLU ASN GLY LYS TYR ALA MET VAL SEQRES 4 A 114 ALA SER LYS GLY GLY ASP PRO LYS HIS PRO SER TRP TYR SEQRES 5 A 114 PHE ASN VAL LYS ALA ASN PRO THR VAL SER VAL GLN ASP SEQRES 6 A 114 GLY ASP LYS VAL LEU PRO ASP ARG THR ALA ARG GLU LEU SEQRES 7 A 114 GLU GLY GLU GLU ARG GLU HIS TRP TRP LYS LEU ALA VAL SEQRES 8 A 114 GLU ALA TYR PRO PRO TYR ALA GLU TYR GLN THR LYS THR SEQRES 9 A 114 ASP ARG LEU ILE PRO VAL PHE ILE VAL GLU HET PO4 A 201 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *188(H2 O) HELIX 1 AA1 SER A 76 ASN A 84 1 9 HELIX 2 AA2 GLU A 105 TYR A 120 1 16 HELIX 3 AA3 PRO A 121 LYS A 129 1 9 SHEET 1 AA1 7 LYS A 48 MET A 54 0 SHEET 2 AA1 7 ILE A 35 THR A 41 -1 N PHE A 38 O VAL A 51 SHEET 3 AA1 7 THR A 86 ASP A 91 -1 O GLN A 90 N LEU A 37 SHEET 4 AA1 7 LYS A 94 GLU A 103 -1 O LEU A 96 N VAL A 89 SHEET 5 AA1 7 VAL A 136 VAL A 139 -1 O ILE A 138 N ARG A 102 SHEET 6 AA1 7 LYS A 61 VAL A 65 -1 N TYR A 62 O VAL A 139 SHEET 7 AA1 7 GLU A 57 GLU A 58 -1 N GLU A 58 O LYS A 61 CISPEP 1 ARG A 33 PRO A 34 0 15.26 SITE 1 AC1 9 GLY A 42 ALA A 43 LYS A 44 SER A 45 SITE 2 AC1 9 ARG A 49 GLU A 105 HOH A 312 HOH A 353 SITE 3 AC1 9 HOH A 378 CRYST1 37.490 36.850 77.591 90.00 96.59 90.00 I 1 2 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 0.026674 0.000000 0.003080 0.00000 SCALE2 0.000000 0.027137 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012974 0.00000