HEADER METAL TRANSPORT 07-MAY-12 4F2E TITLE CRYSTAL STRUCTURE OF THE STREPTOCOCCUS PNEUMONIAE D39 COPPER CHAPERONE TITLE 2 CUPA WITH CU(I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CUPA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 29-123; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 373153; SOURCE 4 STRAIN: D39 / NCTC 7466; SOURCE 5 GENE: SPD0634, SPD_0634; 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: PHIS KEYWDS CUPREDOXIN FOLD, CU(I) CHAPERONE, METAL TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Y.FU,C.E.DANN III,D.P.GIEDROC REVDAT 4 28-FEB-24 4F2E 1 REMARK SEQADV LINK REVDAT 3 06-MAR-13 4F2E 1 JRNL REVDAT 2 13-FEB-13 4F2E 1 JRNL REVDAT 1 30-JAN-13 4F2E 0 JRNL AUTH Y.FU,H.C.TSUI,K.E.BRUCE,L.T.SHAM,K.A.HIGGINS,J.P.LISHER, JRNL AUTH 2 K.M.KAZMIERCZAK,M.J.MARONEY,C.E.DANN,M.E.WINKLER,D.P.GIEDROC JRNL TITL A NEW STRUCTURAL PARADIGM IN COPPER RESISTANCE IN JRNL TITL 2 STREPTOCOCCUS PNEUMONIAE. JRNL REF NAT.CHEM.BIOL. V. 9 177 2013 JRNL REFN ISSN 1552-4450 JRNL PMID 23354287 JRNL DOI 10.1038/NCHEMBIO.1168 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16186 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1619 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 21.0074 - 3.3127 1.00 1322 148 0.1550 0.1606 REMARK 3 2 3.3127 - 2.6310 1.00 1237 137 0.1738 0.2094 REMARK 3 3 2.6310 - 2.2989 1.00 1245 138 0.1797 0.2082 REMARK 3 4 2.2989 - 2.0889 1.00 1226 136 0.1744 0.2006 REMARK 3 5 2.0889 - 1.9393 1.00 1201 133 0.1784 0.2039 REMARK 3 6 1.9393 - 1.8250 1.00 1200 134 0.1618 0.1860 REMARK 3 7 1.8250 - 1.7337 1.00 1212 135 0.1452 0.1852 REMARK 3 8 1.7337 - 1.6582 1.00 1192 133 0.1586 0.1820 REMARK 3 9 1.6582 - 1.5944 1.00 1197 132 0.1814 0.2115 REMARK 3 10 1.5944 - 1.5394 1.00 1179 131 0.2320 0.2458 REMARK 3 11 1.5394 - 1.4913 1.00 1186 132 0.3195 0.3218 REMARK 3 12 1.4913 - 1.4490 0.99 1170 130 0.4584 0.4522 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.61 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 38.51 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.790 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) : 0.65360 REMARK 3 B22 (A**2) : -0.71920 REMARK 3 B33 (A**2) : 0.06560 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 : 0.017 801 REMARK 3 ANGLE : 0.913 1086 REMARK 3 CHIRALITY : 0.061 114 REMARK 3 PLANARITY : 0.004 146 REMARK 3 DIHEDRAL : 11.892 305 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 4F2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072368. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 5.0 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 : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16187 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.449 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.02400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 46.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.18300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% W/V PEG3350, 0.1 M SODIUM CITRATE REMARK 280 TRIBASIC DIHYDRATE, PH 5.0, DEOXY BIG CHAP, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 23.60400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.32350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.60400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.32350 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 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 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 GLU A 106 CG CD OE1 OE2 REMARK 470 LYS A 119 CG CD CE NZ 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 435 O HOH A 474 2.18 REMARK 500 O HOH A 471 O HOH A 474 2.19 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 35 142.23 -170.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU1 A 201 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 74 SG REMARK 620 2 CYS A 111 SG 157.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU1 A 202 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 74 SG REMARK 620 2 MET A 113 SD 128.7 REMARK 620 3 MET A 115 SD 118.3 108.5 REMARK 620 4 CL A 203 CL 100.1 93.2 97.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU1 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU1 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F2F RELATED DB: PDB DBREF 4F2E A 29 123 UNP Q04LG8 Q04LG8_STRP2 29 123 SEQADV 4F2E GLY A 26 UNP Q04LG8 CLONING ARTIFACT SEQADV 4F2E ALA A 27 UNP Q04LG8 CLONING ARTIFACT SEQADV 4F2E MET A 28 UNP Q04LG8 CLONING ARTIFACT SEQRES 1 A 98 GLY ALA MET GLY GLN LYS ALA GLN GLN LYS ASN GLY TYR SEQRES 2 A 98 GLN GLU ILE ARG VAL GLU VAL MET GLY GLY TYR THR PRO SEQRES 3 A 98 GLU LEU ILE VAL LEU LYS LYS SER VAL PRO ALA ARG ILE SEQRES 4 A 98 VAL PHE ASP ARG LYS ASP PRO SER PRO CYS LEU ASP GLN SEQRES 5 A 98 ILE VAL PHE PRO ASP PHE GLY VAL HIS ALA ASN LEU PRO SEQRES 6 A 98 MET GLY GLU GLU TYR VAL VAL GLU ILE THR PRO GLU GLN SEQRES 7 A 98 ALA GLY GLU PHE SER PHE ALA CYS GLY MET ASN MET MET SEQRES 8 A 98 HIS GLY LYS MET ILE VAL GLU HET CU1 A 201 1 HET CU1 A 202 1 HET CL A 203 1 HETNAM CU1 COPPER (I) ION HETNAM CL CHLORIDE ION FORMUL 2 CU1 2(CU 1+) FORMUL 4 CL CL 1- FORMUL 5 HOH *192(H2 O) HELIX 1 1 SER A 72 LEU A 75 5 4 SHEET 1 A 6 GLN A 30 LYS A 31 0 SHEET 2 A 6 LEU A 53 LYS A 57 1 O LEU A 53 N GLN A 30 SHEET 3 A 6 HIS A 117 GLU A 123 1 O ILE A 121 N LEU A 56 SHEET 4 A 6 GLY A 105 CYS A 111 -1 N PHE A 107 O MET A 120 SHEET 5 A 6 GLN A 77 PHE A 80 -1 N VAL A 79 O ALA A 110 SHEET 6 A 6 VAL A 85 ASN A 88 -1 O ALA A 87 N ILE A 78 SHEET 1 B 3 GLN A 33 LYS A 35 0 SHEET 2 B 3 TYR A 38 VAL A 45 -1 O GLU A 40 N GLN A 33 SHEET 3 B 3 TYR A 49 THR A 50 -1 O THR A 50 N GLU A 44 SHEET 1 C 4 GLN A 33 LYS A 35 0 SHEET 2 C 4 TYR A 38 VAL A 45 -1 O GLU A 40 N GLN A 33 SHEET 3 C 4 ALA A 62 ARG A 68 1 O VAL A 65 N VAL A 43 SHEET 4 C 4 GLU A 94 ILE A 99 -1 O ILE A 99 N ALA A 62 LINK SG CYS A 74 CU CU1 A 201 1555 1555 2.16 LINK SG CYS A 74 CU CU1 A 202 1555 1555 2.25 LINK SG CYS A 111 CU CU1 A 201 1555 1555 2.18 LINK SD MET A 113 CU CU1 A 202 1555 1555 2.31 LINK SD MET A 115 CU CU1 A 202 1555 1555 2.32 LINK CU CU1 A 202 CL CL A 203 1555 1555 2.33 CISPEP 1 THR A 50 PRO A 51 0 -2.52 SITE 1 AC1 3 CYS A 74 CYS A 111 CU1 A 202 SITE 1 AC2 5 CYS A 74 MET A 113 MET A 115 CU1 A 201 SITE 2 AC2 5 CL A 203 SITE 1 AC3 4 CYS A 74 MET A 113 MET A 115 CU1 A 202 CRYST1 47.208 78.647 23.455 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 0.021183 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012715 0.000000 0.00000 SCALE3 0.000000 0.000000 0.042635 0.00000