HEADER ELECTRON TRANSPORT 08-MAY-12 4F2I
TITLE CRYSTAL STRUCTURE OF GLUTAREDOXIN-LIKE NRDH FROM MYCOBACTERIUM
TITLE 2 TUBERCULOSIS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: GLUTAREDOXIN NRDH, PUTATIVE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: GLUTAREDOXIN-LIKE ELECTRON TRANSPORTER NRDH, PROBABLE
COMPND 5 GLUTAREDOXIN ELECTRON TRANSPORT COMPONENT OF NRDEF (GLUTAREDOXIN-LIKE
COMPND 6 PROTEIN) NRDH;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS;
SOURCE 3 ORGANISM_TAXID: 83332;
SOURCE 4 STRAIN: H37RV;
SOURCE 5 GENE: MT3139, NRDH, RV3053C, TBSG_00920;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A
KEYWDS THIOREDOXIN FOLD, NRDH, GLUTAREDOXIN, ELECTRON TRANSPORT, REDOX
KEYWDS 2 PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR S.PHULERA,S.C.MANDE
REVDAT 3 08-NOV-23 4F2I 1 REMARK SEQADV
REVDAT 2 26-JUN-13 4F2I 1 JRNL
REVDAT 1 08-MAY-13 4F2I 0
JRNL AUTH S.PHULERA,S.C.MANDE
JRNL TITL THE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS NRDH AT
JRNL TITL 2 0.87 A 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. 1.67 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928)
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) : 1.67
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.23
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7
REMARK 3 NUMBER OF REFLECTIONS : 7997
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.176
REMARK 3 R VALUE (WORKING SET) : 0.172
REMARK 3 FREE R VALUE : 0.212
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.130
REMARK 3 FREE R VALUE TEST SET COUNT : 810
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 26.2332 - 3.0332 1.00 1297 142 0.1706 0.2097
REMARK 3 2 3.0332 - 2.4081 1.00 1215 140 0.1679 0.1996
REMARK 3 3 2.4081 - 2.1038 0.99 1185 136 0.1376 0.1874
REMARK 3 4 2.1038 - 1.9115 0.98 1190 129 0.1376 0.1867
REMARK 3 5 1.9115 - 1.7746 0.98 1152 135 0.1867 0.2407
REMARK 3 6 1.7746 - 1.6700 0.97 1148 128 0.3478 0.3842
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.47
REMARK 3 K_SOL : 0.36
REMARK 3 B_SOL : 37.58
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.520
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) : -0.01290
REMARK 3 B22 (A**2) : -0.66140
REMARK 3 B33 (A**2) : 0.67420
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 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 : 0.010 674
REMARK 3 ANGLE : 1.160 921
REMARK 3 CHIRALITY : 0.067 105
REMARK 3 PLANARITY : 0.007 118
REMARK 3 DIHEDRAL : 13.817 239
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 4F2I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAY-12.
REMARK 100 THE DEPOSITION ID IS D_1000072372.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 22-MAR-11
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7
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 : BRUKER AXS MICROSTAR
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179
REMARK 200 MONOCHROMATOR : MIRRORS
REMARK 200 OPTICS : BRUKER MULTILAYER
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8023
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670
REMARK 200 RESOLUTION RANGE LOW (A) : 35.340
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2
REMARK 200 DATA REDUNDANCY : 7.000
REMARK 200 R MERGE (I) : 0.06400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76
REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3
REMARK 200 DATA REDUNDANCY IN SHELL : 6.70
REMARK 200 R MERGE FOR SHELL (I) : 0.41500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHENIX AUTOBUILD
REMARK 200 STARTING MODEL: 1R7H
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 31.68
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 3350, 0.15M AMMONIUM NITRATE,
REMARK 280 PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
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 26.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.09000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.09000
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: 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 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 237 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 277 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 279 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 VAL A 54
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 265 O HOH A 270 1.90
REMARK 500 O HOH A 252 O HOH A 253 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 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -3.0 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 A 81 56.11 -162.95
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 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 102
DBREF 4F2I A 2 79 UNP P95106 P95106_MYCTU 2 79
SEQADV 4F2I HIS A 80 UNP P95106 EXPRESSION TAG
SEQADV 4F2I HIS A 81 UNP P95106 EXPRESSION TAG
SEQADV 4F2I HIS A 82 UNP P95106 EXPRESSION TAG
SEQADV 4F2I HIS A 83 UNP P95106 EXPRESSION TAG
SEQADV 4F2I HIS A 84 UNP P95106 EXPRESSION TAG
SEQADV 4F2I HIS A 85 UNP P95106 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 A 101 4
HET NO3 A 102 4
HETNAM NO3 NITRATE ION
FORMUL 2 NO3 2(N O3 1-)
FORMUL 4 HOH *83(H2 O)
HELIX 1 1 CYS A 11 GLN A 24 1 14
HELIX 2 2 ASP A 36 GLY A 47 1 12
HELIX 3 3 ARG A 65 ALA A 71 1 7
HELIX 4 4 ALA A 71 ALA A 76 1 6
SHEET 1 A 3 GLN A 29 ASP A 32 0
SHEET 2 A 3 VAL A 3 THR A 7 1 N VAL A 3 O GLN A 29
SHEET 3 A 3 VAL A 53 VAL A 53 -1 O VAL A 53 N TYR A 6
SSBOND 1 CYS A 11 CYS A 14 1555 1555 2.07
CISPEP 1 ALA A 51 PRO A 52 0 -4.12
SITE 1 AC1 8 TYR A 48 LEU A 49 GLN A 50 SER A 62
SITE 2 AC1 8 ALA A 79 HIS A 81 HOH A 225 HOH A 236
SITE 1 AC2 5 ARG A 65 PRO A 66 ASP A 67 ARG A 68
SITE 2 AC2 5 HOH A 256
CRYST1 52.000 48.180 26.230 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 0.019231 0.000000 0.000000 0.00000
SCALE2 0.000000 0.020756 0.000000 0.00000
SCALE3 0.000000 0.000000 0.038124 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
