HEADER OXIDOREDUCTASE 28-MAR-11 3RAZ TITLE THE CRYSTAL STRUCTURE OF THIOREDOXIN-RELATED PROTEIN FROM NEISSERIA TITLE 2 MENINGITIDIS SEROGROUP B COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN-RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS SEROGROUP B; SOURCE 3 ORGANISM_TAXID: 491; SOURCE 4 GENE: NMB0006; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-CODON+RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: BC - PSGX3 (BC) KEYWDS STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NEW YORK KEYWDS 2 SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, NYSGXRC, THIOREDOXIN- KEYWDS 3 RELATED PROTEIN, REDOXIN, SGX, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.ZHANG,S.K.BURLEY,S.SWAMINATHAN,NEW YORK SGX RESEARCH CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (NYSGXRC) REVDAT 2 10-FEB-21 3RAZ 1 AUTHOR JRNL SEQADV LINK REVDAT 1 11-MAY-11 3RAZ 0 JRNL AUTH Z.ZHANG,S.K.BURLEY,S.SWAMINATHAN JRNL TITL THE CRYSTAL STRUCTURE OF THIOREDOXIN-RELATED PROTEIN FROM JRNL TITL 2 NEISSERIA MENINGITIDIS SEROGROUP B JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.190 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 9567 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 461 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 43.5229 - 2.8844 0.99 3078 160 0.2126 0.2404 REMARK 3 2 2.8844 - 2.2895 0.99 3033 167 0.2603 0.3341 REMARK 3 3 2.2895 - 2.0001 0.97 2995 134 0.2671 0.3564 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 : 0.35 REMARK 3 B_SOL : 40.22 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.87880 REMARK 3 B22 (A**2) : 12.28270 REMARK 3 B33 (A**2) : -10.40380 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.66520 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 : 0.009 1082 REMARK 3 ANGLE : 1.188 1467 REMARK 3 CHIRALITY : 0.070 161 REMARK 3 PLANARITY : 0.008 184 REMARK 3 DIHEDRAL : 16.460 393 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 3RAZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000064707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9567 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 43.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.17100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 8.5, 30% PEG 4K, 2.4 REMARK 280 M LITHIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 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 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 24.22150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.51650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 24.22150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.51650 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 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 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 MSE A 18 REMARK 465 SER A 19 REMARK 465 LEU A 20 REMARK 465 SER A 21 REMARK 465 ALA A 22 REMARK 465 ASP A 23 REMARK 465 CYS A 159 REMARK 465 ARG A 160 REMARK 465 GLU A 161 REMARK 465 GLY A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-11210D RELATED DB: TARGETDB DBREF 3RAZ A 21 160 UNP Q9K1R4 Q9K1R4_NEIMB 21 160 SEQADV 3RAZ MSE A 18 UNP Q9K1R4 EXPRESSION TAG SEQADV 3RAZ SER A 19 UNP Q9K1R4 EXPRESSION TAG SEQADV 3RAZ LEU A 20 UNP Q9K1R4 EXPRESSION TAG SEQADV 3RAZ GLU A 161 UNP Q9K1R4 EXPRESSION TAG SEQADV 3RAZ GLY A 162 UNP Q9K1R4 EXPRESSION TAG SEQADV 3RAZ HIS A 163 UNP Q9K1R4 EXPRESSION TAG SEQADV 3RAZ HIS A 164 UNP Q9K1R4 EXPRESSION TAG SEQADV 3RAZ HIS A 165 UNP Q9K1R4 EXPRESSION TAG SEQADV 3RAZ HIS A 166 UNP Q9K1R4 EXPRESSION TAG SEQADV 3RAZ HIS A 167 UNP Q9K1R4 EXPRESSION TAG SEQADV 3RAZ HIS A 168 UNP Q9K1R4 EXPRESSION TAG SEQRES 1 A 151 MSE SER LEU SER ALA ASP GLU LEU ALA GLY TRP LYS ASP SEQRES 2 A 151 ASN THR PRO GLN SER LEU GLN SER LEU LYS ALA PRO VAL SEQRES 3 A 151 ARG ILE VAL ASN LEU TRP ALA THR TRP CYS GLY PRO CYS SEQRES 4 A 151 ARG LYS GLU MSE PRO ALA MSE SER LYS TRP TYR LYS ALA SEQRES 5 A 151 GLN LYS LYS GLY SER VAL ASP MSE VAL GLY ILE ALA LEU SEQRES 6 A 151 ASP THR SER ASP ASN ILE GLY ASN PHE LEU LYS GLN THR SEQRES 7 A 151 PRO VAL SER TYR PRO ILE TRP ARG TYR THR GLY ALA ASN SEQRES 8 A 151 SER ARG ASN PHE MSE LYS THR TYR GLY ASN THR VAL GLY SEQRES 9 A 151 VAL LEU PRO PHE THR VAL VAL GLU ALA PRO LYS CYS GLY SEQRES 10 A 151 TYR ARG GLN THR ILE THR GLY GLU VAL ASN GLU LYS SER SEQRES 11 A 151 LEU THR ASP ALA VAL LYS LEU ALA HIS SER LYS CYS ARG SEQRES 12 A 151 GLU GLY HIS HIS HIS HIS HIS HIS MODRES 3RAZ MSE A 60 MET SELENOMETHIONINE MODRES 3RAZ MSE A 63 MET SELENOMETHIONINE MODRES 3RAZ MSE A 77 MET SELENOMETHIONINE MODRES 3RAZ MSE A 113 MET SELENOMETHIONINE HET MSE A 60 8 HET MSE A 63 8 HET MSE A 77 8 HET MSE A 113 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 HOH *33(H2 O) HELIX 1 1 SER A 35 LEU A 39 5 5 HELIX 2 2 CYS A 53 ALA A 69 1 17 HELIX 3 3 THR A 84 THR A 95 1 12 HELIX 4 4 ASN A 108 THR A 115 1 8 HELIX 5 5 ASN A 144 SER A 157 1 14 SHEET 1 A 7 PRO A 33 GLN A 34 0 SHEET 2 A 7 LEU A 25 GLY A 27 -1 N LEU A 25 O GLN A 34 SHEET 3 A 7 ILE A 101 TYR A 104 -1 O ARG A 103 N ALA A 26 SHEET 4 A 7 VAL A 75 ALA A 81 1 N ALA A 81 O TRP A 102 SHEET 5 A 7 VAL A 43 TRP A 49 1 N ASN A 47 O ILE A 80 SHEET 6 A 7 PHE A 125 ALA A 130 -1 O PHE A 125 N LEU A 48 SHEET 7 A 7 TYR A 135 THR A 138 -1 O GLN A 137 N VAL A 128 SSBOND 1 CYS A 53 CYS A 56 1555 1555 2.06 LINK C GLU A 59 N MSE A 60 1555 1555 1.33 LINK C MSE A 60 N PRO A 61 1555 1555 1.34 LINK C ALA A 62 N MSE A 63 1555 1555 1.33 LINK C MSE A 63 N SER A 64 1555 1555 1.33 LINK C ASP A 76 N MSE A 77 1555 1555 1.33 LINK C MSE A 77 N VAL A 78 1555 1555 1.33 LINK C PHE A 112 N MSE A 113 1555 1555 1.33 LINK C MSE A 113 N LYS A 114 1555 1555 1.33 CISPEP 1 LEU A 123 PRO A 124 0 4.58 CRYST1 48.443 69.033 45.032 90.00 104.93 90.00 C 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 0.020643 0.000000 0.005503 0.00000 SCALE2 0.000000 0.014486 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022982 0.00000