HEADER METAL BINDING PROTEIN 18-DEC-15 5FFD TITLE COPM IN THE AG-BOUND FORM (BY CO-CRYSTALLIZATION) COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPM; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP. PCC 6803; SOURCE 3 ORGANISM_TAXID: 1148; SOURCE 4 GENE: PCOPM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS COPPER BINDING PROTEIN, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.ZHAO,X.WANG,L.LIU REVDAT 3 08-NOV-23 5FFD 1 REMARK REVDAT 2 25-DEC-19 5FFD 1 JRNL REMARK REVDAT 1 07-SEP-16 5FFD 0 JRNL AUTH S.ZHAO,X.WANG,G.NIU,W.DONG,J.WANG,Y.FANG,Y.LIN,L.LIU JRNL TITL STRUCTURAL BASIS FOR COPPER/SILVER BINDING BY THE JRNL TITL 2 SYNECHOCYSTIS METALLOCHAPERONE COPM. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 72 997 2016 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 27599732 JRNL DOI 10.1107/S2059798316011943 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 33.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 25108 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1263 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 33.6062 - 3.0166 0.98 2974 149 0.1689 0.1840 REMARK 3 2 3.0166 - 2.3946 0.99 2847 151 0.1585 0.1862 REMARK 3 3 2.3946 - 2.0919 1.00 2825 151 0.1394 0.1834 REMARK 3 4 2.0919 - 1.9007 1.00 2821 156 0.1516 0.1945 REMARK 3 5 1.9007 - 1.7645 1.00 2783 154 0.1432 0.1959 REMARK 3 6 1.7645 - 1.6604 0.99 2771 161 0.1502 0.2066 REMARK 3 7 1.6604 - 1.5773 0.96 2667 150 0.1505 0.2280 REMARK 3 8 1.5773 - 1.5086 0.84 2347 114 0.1503 0.2322 REMARK 3 9 1.5086 - 1.4506 0.64 1810 77 0.1680 0.2197 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.008 1217 REMARK 3 ANGLE : 0.816 1641 REMARK 3 CHIRALITY : 0.060 167 REMARK 3 PLANARITY : 0.004 216 REMARK 3 DIHEDRAL : 13.416 475 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 5FFD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000216460. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-15 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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26798 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 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) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.47400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, PHASER REMARK 200 STARTING MODEL: 3BT5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES 6.0, 20% PEG 2000 MME, 1MM REMARK 280 AGNO3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 26.93600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.97950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.93600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.97950 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 TOTAL BURIED SURFACE AREA: 250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 GLY A 25 REMARK 465 SER A 26 REMARK 465 ARG A 27 REMARK 465 ASN A 28 REMARK 465 GLN A 29 REMARK 465 SER A 30 REMARK 465 PRO A 31 REMARK 465 PRO A 32 REMARK 465 GLN A 33 REMARK 465 MET A 34 REMARK 465 MET A 35 REMARK 465 ALA A 36 REMARK 465 GLN A 37 REMARK 465 GLN A 38 REMARK 465 GLY A 39 REMARK 465 MET A 40 REMARK 465 HIS A 41 REMARK 465 MET A 42 REMARK 465 LEU A 109 REMARK 465 SER A 110 REMARK 465 SER A 111 REMARK 465 GLN A 112 REMARK 465 GLY A 113 REMARK 465 MET A 114 REMARK 465 MET A 115 REMARK 465 GLY A 116 REMARK 465 MET A 117 REMARK 465 HIS A 118 REMARK 465 GLN A 119 REMARK 465 GLY A 120 REMARK 465 HIS A 121 REMARK 465 GLY A 122 REMARK 465 MET A 123 REMARK 465 MET A 124 REMARK 465 GLN A 196 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 A 70 CE NZ REMARK 470 LYS A 95 CG CD CE NZ REMARK 470 ASP A 129 CG OD1 OD2 REMARK 470 LYS A 170 CD CE NZ REMARK 470 LYS A 184 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 416 O HOH A 449 2.18 REMARK 500 O HOH A 488 O HOH A 514 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 515 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A 516 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A 517 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A 518 DISTANCE = 6.51 ANGSTROMS 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 AG A 201 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 56 ND1 REMARK 620 2 HIS A 57 ND1 172.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG A 202 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 148 ND1 REMARK 620 2 HIS A 149 ND1 173.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AG A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FEJ RELATED DB: PDB REMARK 900 RELATED ID: 5FFA RELATED DB: PDB REMARK 900 RELATED ID: 5FFB RELATED DB: PDB REMARK 900 RELATED ID: 5FFC RELATED DB: PDB REMARK 900 RELATED ID: 5FFE RELATED DB: PDB DBREF1 5FFD A 27 196 UNP A0A0F6QDN6_9SYNC DBREF2 5FFD A A0A0F6QDN6 27 196 SEQADV 5FFD GLY A 25 UNP A0A0F6QDN EXPRESSION TAG SEQADV 5FFD SER A 26 UNP A0A0F6QDN EXPRESSION TAG SEQRES 1 A 172 GLY SER ARG ASN GLN SER PRO PRO GLN MET MET ALA GLN SEQRES 2 A 172 GLN GLY MET HIS MET GLN TRP THR ASP GLN SER PHE ILE SEQRES 3 A 172 GLU MET MET THR PRO HIS HIS GLN ASP ALA ILE ASP MET SEQRES 4 A 172 ALA GLU MET ALA LEU GLN LYS ALA GLU HIS PRO GLU LEU SEQRES 5 A 172 LYS LYS LEU ALA ARG ASN ILE ILE ARG ASP GLN GLU ARG SEQRES 6 A 172 GLU ILE LYS GLU MET LYS THR TRP TYR GLN GLN TRP PHE SEQRES 7 A 172 LYS ARG PRO VAL PRO ALA LEU SER SER GLN GLY MET MET SEQRES 8 A 172 GLY MET HIS GLN GLY HIS GLY MET MET ALA MET ASP LEU SEQRES 9 A 172 ASP ALA LEU ALA THR ALA GLN ASN PHE ASP ARG GLU PHE SEQRES 10 A 172 ILE ARG GLN MET ILE PRO HIS HIS GLN MET ALA VAL MET SEQRES 11 A 172 MET ALA SER ASN LEU LYS THR ASN THR GLU ARG PRO GLU SEQRES 12 A 172 MET ASP LYS LEU MET ASP ASP ILE ILE ARG SER GLN SER SEQRES 13 A 172 ALA GLU ILE LYS GLN MET LYS GLN TRP TYR GLN ASN TRP SEQRES 14 A 172 TYR GLY GLN HET AG A 201 1 HET AG A 202 1 HET AG A 203 1 HETNAM AG SILVER ION FORMUL 2 AG 3(AG 1+) FORMUL 5 HOH *218(H2 O) HELIX 1 AA1 THR A 45 ALA A 71 1 27 HELIX 2 AA2 HIS A 73 LYS A 103 1 31 HELIX 3 AA3 ASP A 127 ALA A 134 1 8 HELIX 4 AA4 ASN A 136 THR A 163 1 28 HELIX 5 AA5 ARG A 165 GLY A 195 1 31 LINK ND1 HIS A 56 AG AG A 201 1555 1555 2.22 LINK ND1 HIS A 57 AG AG A 201 1555 1555 2.16 LINK ND1 HIS A 148 AG AG A 202 1555 1555 2.17 LINK ND1 HIS A 149 AG AG A 202 1555 1555 2.15 SITE 1 AC1 4 MET A 53 HIS A 56 HIS A 57 HOH A 370 SITE 1 AC2 4 MET A 145 HIS A 148 HIS A 149 HOH A 370 SITE 1 AC3 4 MET A 151 MET A 155 HOH A 488 HOH A 514 CRYST1 53.872 85.959 31.729 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 0.018563 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011633 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031517 0.00000