HEADER ELECTRON TRANSPORT 18-APR-13 4K8M TITLE HIGH RESOLUTION STRUCTURE OF M.TB NRDH COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN-LIKE PROTEIN NRDH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: RV3053C, RVBD_3053C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS THIOREDOXIN, REDOXIN, THIOREDOXIN REDUCTASE, RIBONUCLEOTIDE KEYWDS 2 REDUCTASE, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.PHULERA,S.C.MANDE REVDAT 3 08-NOV-23 4K8M 1 REMARK SEQADV REVDAT 2 23-JUL-14 4K8M 1 REMARK REVDAT 1 18-JUN-14 4K8M 0 JRNL AUTH S.PHULERA,S.C.MANDE JRNL TITL THE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS NRDH AT JRNL TITL 2 0.87 ANGSTROM SUGGESTS A POSSIBLE MODE OF ITS ACTIVITY. JRNL REF BIOCHEMISTRY V. 52 4056 2013 JRNL REFN ISSN 0006-2960 JRNL PMID 23675692 JRNL DOI 10.1021/BI400191Z REMARK 2 REMARK 2 RESOLUTION. 0.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.140 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1985 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 630 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 99 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4K8M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079028. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-12 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 : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.71255 REMARK 200 MONOCHROMATOR : BAND PASS 1.9X10-4 FOR A SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARCCD 225X225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53538 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.870 REMARK 200 RESOLUTION RANGE LOW (A) : 23.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: 4F2I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 25.79750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.85250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.79750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.85250 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A1019 CE NZ REMARK 470 LYS A1023 CE NZ REMARK 470 GLN A1050 CD OE1 NE2 REMARK 470 HIS A1085 CG ND1 CD2 CE1 NE2 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 SER A1015 N - CA - CB ANGL. DEV. = -9.8 DEGREES REMARK 500 LYS A1019 CA - C - O ANGL. DEV. = 16.2 DEGREES REMARK 500 LYS A1019 CA - C - O ANGL. DEV. = 20.4 DEGREES REMARK 500 LYS A1019 CA - C - N ANGL. DEV. = -13.4 DEGREES REMARK 500 LYS A1019 CA - C - N ANGL. DEV. = -17.3 DEGREES REMARK 500 ARG A1040 NH1 - CZ - NH2 ANGL. DEV. = 8.5 DEGREES REMARK 500 ARG A1040 NE - CZ - NH1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A1040 NE - CZ - NH1 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG A1040 NE - CZ - NH2 ANGL. DEV. = -7.3 DEGREES REMARK 500 MET A1044 CA - CB - CG ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG A1065 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A1065 NE - CZ - NH2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG A1068 NE - CZ - NH1 ANGL. DEV. = 4.3 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 HIS A1081 51.41 -160.56 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 NO3 A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 2003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 2005 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F2I RELATED DB: PDB REMARK 900 1.67 ANGSTROM RESOLUTION STRUCTURE WHERE DIFFRACTION DATA WERE REMARK 900 COLLECTED ON IN-HOUSE SOURCE REMARK 900 RELATED ID: 4HS1 RELATED DB: PDB REMARK 900 0.87 ANGSTROM STRUCTURE REFINED USING PHENIX AND REFMAC DBREF 4K8M A 1002 1079 UNP I6YB06 I6YB06_MYCTU 2 79 SEQADV 4K8M HIS A 1080 UNP I6YB06 EXPRESSION TAG SEQADV 4K8M HIS A 1081 UNP I6YB06 EXPRESSION TAG SEQADV 4K8M HIS A 1082 UNP I6YB06 EXPRESSION TAG SEQADV 4K8M HIS A 1083 UNP I6YB06 EXPRESSION TAG SEQADV 4K8M HIS A 1084 UNP I6YB06 EXPRESSION TAG SEQADV 4K8M HIS A 1085 UNP I6YB06 EXPRESSION TAG SEQRES 1 A 84 THR VAL THR VAL TYR THR LYS PRO ALA CYS VAL GLN CYS SEQRES 2 A 84 SER ALA THR SER LYS ALA LEU ASP LYS GLN GLY ILE ALA SEQRES 3 A 84 TYR GLN LYS VAL ASP ILE SER LEU ASP SER GLU ALA ARG SEQRES 4 A 84 ASP TYR VAL MET ALA LEU GLY TYR LEU GLN ALA PRO VAL SEQRES 5 A 84 VAL VAL ALA GLY ASN ASP HIS TRP SER GLY PHE ARG PRO SEQRES 6 A 84 ASP ARG ILE LYS ALA LEU ALA GLY ALA ALA LEU THR ALA SEQRES 7 A 84 HIS HIS HIS HIS HIS HIS HET NO3 A2001 4 HET NO3 A2002 4 HET CL A2003 1 HET GOL A2004 6 HET PEG A2005 7 HETNAM NO3 NITRATE ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NO3 2(N O3 1-) FORMUL 4 CL CL 1- FORMUL 5 GOL C3 H8 O3 FORMUL 6 PEG C4 H10 O3 FORMUL 7 HOH *99(H2 O) HELIX 1 1 CYS A 1011 GLN A 1024 1 14 HELIX 2 2 ASP A 1036 GLY A 1047 1 12 HELIX 3 3 ARG A 1065 ALA A 1071 1 7 HELIX 4 4 ALA A 1071 ALA A 1076 1 6 SHEET 1 A 4 GLN A1029 ASP A1032 0 SHEET 2 A 4 VAL A1003 THR A1007 1 N VAL A1003 O GLN A1029 SHEET 3 A 4 VAL A1053 ALA A1056 -1 O VAL A1053 N TYR A1006 SHEET 4 A 4 ASP A1059 SER A1062 -1 O TRP A1061 N VAL A1054 SSBOND 1 CYS A 1011 CYS A 1014 1555 1555 2.07 CISPEP 1 ALA A 1051 PRO A 1052 0 -5.59 SITE 1 AC1 5 ARG A1065 PRO A1066 ASP A1067 ARG A1068 SITE 2 AC1 5 HOH A4058 SITE 1 AC2 7 TYR A1048 LEU A1049 GLN A1050 SER A1062 SITE 2 AC2 7 ALA A1079 HIS A1081 HOH A4041 SITE 1 AC3 4 TYR A1048 HIS A1060 HOH A4033 HOH A4063 SITE 1 AC4 8 VAL A1012 GLN A1013 MET A1044 HIS A1083 SITE 2 AC4 8 HOH A4006 HOH A4007 HOH A4008 HOH A4014 SITE 1 AC5 12 THR A1007 LYS A1008 ALA A1010 CYS A1011 SITE 2 AC5 12 CYS A1014 SER A1015 SER A1018 LYS A1030 SITE 3 AC5 12 GLU A1038 HIS A1084 HOH A4031 HOH A4097 CRYST1 51.595 47.705 26.050 90.00 90.00 90.00 P 21 21 2 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 0.019382 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020962 0.000000 0.00000 SCALE3 0.000000 0.000000 0.038388 0.00000