HEADER OXIDOREDUCTASE 26-APR-12 4EVM TITLE 1.5 ANGSTROM CRYSTAL STRUCTURE OF SOLUBLE DOMAIN OF MEMBRANE-ANCHORED TITLE 2 THIOREDOXIN FAMILY PROTEIN FROM STREPTOCOCCUS PNEUMONIAE STRAIN TITLE 3 CANADA MDR_19A COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 51-188; COMPND 5 EC: 1.8.4.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313; SOURCE 4 STRAIN: MDR_19A; SOURCE 5 GENE: SPNECM_010100000757, SP_0659; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P15TV LIC KEYWDS STRUCTURAL GENOMICS, NIAID, NATIONAL INSTITUTE OF ALLERGY AND KEYWDS 2 INFECTIOUS DISEASES, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS KEYWDS 3 DISEASES, CSGID, ALPHA/BETA PROTEIN, THIOREDOXIN FOLD, THIOREDOXIN- KEYWDS 4 LIKE SUPERFAMILY, TLPA-LIKE FAMILY, GLUTATHIONE PEROXIDASE-LIKE KEYWDS 5 FAMILY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.WAWRZAK,P.J.STOGIOS,G.MINASOV,M.KUDRITSKA,V.YIM,A.SAVCHENKO, AUTHOR 2 W.F.ANDERSON,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES AUTHOR 3 (CSGID) REVDAT 3 16-OCT-24 4EVM 1 REMARK REVDAT 2 13-SEP-23 4EVM 1 REMARK REVDAT 1 09-MAY-12 4EVM 0 JRNL AUTH Z.WAWRZAK,P.J.STOGIOS,G.MINASOV,M.KUDRITSKA,V.YIM, JRNL AUTH 2 A.SAVCHENKO,W.F.ANDERSON, JRNL AUTH 3 CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES JRNL AUTH 4 (CSGID) JRNL TITL 1.5 ANGSTROM CRYSTAL STRUCTURE OF SOLUBLE DOMAIN OF JRNL TITL 2 MEMBRANE-ANCHORED THIOREDOXIN FAMILY PROTEIN FROM JRNL TITL 3 STREPTOCOCCUS PNEUMONIAE STRAIN CANADA MDR_19A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.51 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) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 29395 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1419 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 29.8365 - 4.0151 0.97 2688 134 0.1627 0.1805 REMARK 3 2 4.0151 - 3.1881 1.00 2755 147 0.1580 0.1753 REMARK 3 3 3.1881 - 2.7855 1.00 2751 144 0.1666 0.2299 REMARK 3 4 2.7855 - 2.5309 1.00 2750 143 0.1629 0.1932 REMARK 3 5 2.5309 - 2.3496 1.00 2754 149 0.1645 0.1780 REMARK 3 6 2.3496 - 2.2111 1.00 2773 148 0.1617 0.1781 REMARK 3 7 2.2111 - 2.1004 1.00 2751 147 0.1686 0.2079 REMARK 3 8 2.1004 - 2.0090 1.00 2767 145 0.1754 0.1920 REMARK 3 9 2.0090 - 1.9317 1.00 2746 141 0.1723 0.2246 REMARK 3 10 1.9317 - 1.8650 1.00 2739 144 0.1705 0.2240 REMARK 3 11 1.8650 - 1.8067 1.00 2766 142 0.1709 0.2306 REMARK 3 12 1.8067 - 1.7551 1.00 2761 143 0.1760 0.1924 REMARK 3 13 1.7551 - 1.7089 1.00 2748 144 0.1850 0.2300 REMARK 3 14 1.7089 - 1.6672 1.00 2749 143 0.1981 0.2668 REMARK 3 15 1.6672 - 1.6293 1.00 2774 145 0.2050 0.2435 REMARK 3 16 1.6293 - 1.5946 1.00 2776 143 0.1957 0.2160 REMARK 3 17 1.5946 - 1.5627 1.00 2755 144 0.2061 0.2227 REMARK 3 18 1.5627 - 1.5332 1.00 2761 146 0.2170 0.2577 REMARK 3 19 1.5332 - 1.5060 0.94 2565 133 0.2323 0.2480 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 58.26 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.130 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) : 1.09710 REMARK 3 B22 (A**2) : 1.09710 REMARK 3 B33 (A**2) : -2.19420 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 : 0.013 1244 REMARK 3 ANGLE : 1.436 1709 REMARK 3 CHIRALITY : 0.095 189 REMARK 3 PLANARITY : 0.007 220 REMARK 3 DIHEDRAL : 13.819 487 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 51:70 REMARK 3 ORIGIN FOR THE GROUP (A): 22.4441 53.2607 48.7657 REMARK 3 T TENSOR REMARK 3 T11: 0.3272 T22: 0.2207 REMARK 3 T33: 0.1437 T12: -0.0573 REMARK 3 T13: 0.0136 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 6.3699 L22: 2.7442 REMARK 3 L33: 4.3874 L12: 2.3923 REMARK 3 L13: -1.4378 L23: -0.3636 REMARK 3 S TENSOR REMARK 3 S11: 0.1890 S12: -0.7872 S13: -0.3362 REMARK 3 S21: 0.5270 S22: -0.4275 S23: -0.3773 REMARK 3 S31: 0.4796 S32: 0.1258 S33: 0.1752 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 71:135 REMARK 3 ORIGIN FOR THE GROUP (A): 19.2010 54.2011 34.7220 REMARK 3 T TENSOR REMARK 3 T11: 0.1316 T22: 0.0982 REMARK 3 T33: 0.1361 T12: 0.0053 REMARK 3 T13: 0.0432 T23: -0.0300 REMARK 3 L TENSOR REMARK 3 L11: 3.6728 L22: 2.9394 REMARK 3 L33: 3.6356 L12: 1.2857 REMARK 3 L13: -1.0156 L23: -0.7093 REMARK 3 S TENSOR REMARK 3 S11: 0.0423 S12: -0.0061 S13: 0.2111 REMARK 3 S21: 0.2171 S22: -0.0701 S23: 0.3062 REMARK 3 S31: 0.0171 S32: -0.1938 S33: 0.0158 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 136:188 REMARK 3 ORIGIN FOR THE GROUP (A): 18.1256 44.0369 38.2443 REMARK 3 T TENSOR REMARK 3 T11: 0.2183 T22: 0.1150 REMARK 3 T33: 0.1013 T12: -0.0046 REMARK 3 T13: 0.0203 T23: 0.0087 REMARK 3 L TENSOR REMARK 3 L11: 5.4628 L22: 3.7081 REMARK 3 L33: 2.1926 L12: 1.9654 REMARK 3 L13: -0.2022 L23: 0.3160 REMARK 3 S TENSOR REMARK 3 S11: 0.1001 S12: -0.2036 S13: -0.3527 REMARK 3 S21: 0.2605 S22: -0.1484 S23: 0.0387 REMARK 3 S31: 0.3799 S32: -0.1436 S33: 0.0614 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 4EVM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000072124. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-12 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 : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29395 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 40.2200 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) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.57900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.110 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 2H30 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% W/V PEG3350, 0.2 M MAGNESIUM REMARK 280 CHLORIDE, 0.1 M TRIS-CL, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 44.93600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.62350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.62350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.40400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.62350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.62350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.46800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.62350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.62350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.40400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.62350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.62350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.46800 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 44.93600 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: CSGID-IDP91959 RELATED DB: TARGETTRACK DBREF 4EVM A 51 188 UNP Q97RX4 Q97RX4_STRPN 51 188 SEQRES 1 A 138 GLU VAL ALA ASP PHE GLU LEU MET GLY VAL ASP GLY LYS SEQRES 2 A 138 THR TYR ARG LEU SER ASP TYR LYS GLY LYS LYS VAL TYR SEQRES 3 A 138 LEU LYS PHE TRP ALA SER TRP CYS SER ILE CYS LEU ALA SEQRES 4 A 138 SER LEU PRO ASP THR ASP GLU ILE ALA LYS GLU ALA GLY SEQRES 5 A 138 ASP ASP TYR VAL VAL LEU THR VAL VAL SER PRO GLY HIS SEQRES 6 A 138 LYS GLY GLU GLN SER GLU ALA ASP PHE LYS ASN TRP TYR SEQRES 7 A 138 LYS GLY LEU ASP TYR LYS ASN LEU PRO VAL LEU VAL ASP SEQRES 8 A 138 PRO SER GLY LYS LEU LEU GLU THR TYR GLY VAL ARG SER SEQRES 9 A 138 TYR PRO THR GLN ALA PHE ILE ASP LYS GLU GLY LYS LEU SEQRES 10 A 138 VAL LYS THR HIS PRO GLY PHE MET GLU LYS ASP ALA ILE SEQRES 11 A 138 LEU GLN THR LEU LYS GLU LEU ALA FORMUL 2 HOH *207(H2 O) HELIX 1 1 SER A 68 LYS A 71 5 4 HELIX 2 2 CYS A 84 GLU A 100 1 17 HELIX 3 3 SER A 120 LYS A 129 1 10 HELIX 4 4 GLY A 144 TYR A 150 1 7 HELIX 5 5 GLU A 176 LEU A 187 1 12 SHEET 1 A 2 GLU A 56 MET A 58 0 SHEET 2 A 2 THR A 64 ARG A 66 -1 O TYR A 65 N LEU A 57 SHEET 1 B 5 VAL A 138 VAL A 140 0 SHEET 2 B 5 TYR A 105 VAL A 111 1 N THR A 109 O LEU A 139 SHEET 3 B 5 LYS A 74 PHE A 79 1 N TYR A 76 O VAL A 106 SHEET 4 B 5 THR A 157 ILE A 161 -1 O THR A 157 N PHE A 79 SHEET 5 B 5 LEU A 167 PRO A 172 -1 O VAL A 168 N PHE A 160 SSBOND 1 CYS A 84 CYS A 87 1555 1555 2.12 CISPEP 1 TYR A 155 PRO A 156 0 -9.25 CRYST1 63.247 63.247 89.872 90.00 90.00 90.00 P 43 21 2 8 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 0.015811 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015811 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011127 0.00000