HEADER METAL BINDING PROTEIN 19-MAY-19 6P17 TITLE APO PCUAC DOMAIN FROM PMOF1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PMOF1; COMPND 3 CHAIN: B, A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOCYSTIS SP. ATCC 49242; SOURCE 3 ORGANISM_TAXID: 622637; SOURCE 4 GENE: MET49242_1449; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COPPER BINDING PROTEIN, CHAPERONE, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.R.SENDZIK,O.S.FISHER,A.C.ROSENZWEIG REVDAT 5 11-OCT-23 6P17 1 REMARK REVDAT 4 04-DEC-19 6P17 1 REMARK REVDAT 3 13-NOV-19 6P17 1 JRNL REVDAT 2 02-OCT-19 6P17 1 JRNL REVDAT 1 25-SEP-19 6P17 0 JRNL AUTH O.S.FISHER,M.R.SENDZIK,M.O.ROSS,T.J.LAWTON,B.M.HOFFMAN, JRNL AUTH 2 A.C.ROSENZWEIG JRNL TITL PCUAC DOMAINS FROM METHANE-OXIDIZING BACTERIA USE A JRNL TITL 2 HISTIDINE BRACE TO BIND COPPER. JRNL REF J.BIOL.CHEM. V. 294 16351 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31527086 JRNL DOI 10.1074/JBC.RA119.010093 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 21136 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.440 REMARK 3 FREE R VALUE TEST SET COUNT : 1996 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 37.4561 - 4.4600 0.99 1499 155 0.2080 0.2387 REMARK 3 2 4.4600 - 3.5409 0.99 1420 147 0.1935 0.2451 REMARK 3 3 3.5409 - 3.0936 0.95 1354 141 0.2087 0.2619 REMARK 3 4 3.0936 - 2.8108 0.99 1391 146 0.2409 0.3047 REMARK 3 5 2.8108 - 2.6094 0.99 1386 144 0.2488 0.3257 REMARK 3 6 2.6094 - 2.4556 0.99 1388 144 0.2393 0.3132 REMARK 3 7 2.4556 - 2.3326 0.99 1374 145 0.2285 0.2834 REMARK 3 8 2.3326 - 2.2311 0.99 1368 143 0.2285 0.2519 REMARK 3 9 2.2311 - 2.1452 0.99 1357 141 0.2294 0.2534 REMARK 3 10 2.1452 - 2.0712 0.99 1352 142 0.2314 0.2925 REMARK 3 11 2.0712 - 2.0064 0.96 1334 139 0.2337 0.3013 REMARK 3 12 2.0064 - 1.9491 0.98 1333 139 0.2533 0.2888 REMARK 3 13 1.9491 - 1.8978 0.98 1336 140 0.2928 0.3381 REMARK 3 14 1.8978 - 1.8515 0.91 1248 130 0.3738 0.4377 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.87 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6P17 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1000241683. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.373 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21609 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 37.448 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 3.451 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.41 REMARK 200 R MERGE FOR SHELL (I) : 1.04300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.140 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: PDB ENTRY 6P1E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, 0.2 M AMMONIUM REMARK 280 ACETATE, 34% PEG4000, PH 4.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.82100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.55000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.28950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.55000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.82100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.28950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: B 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 350 REMARK 350 BIOMOLECULE: 2 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 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 SER B 31 REMARK 465 MET B 32 REMARK 465 ASP B 153 REMARK 465 SER A 31 REMARK 465 MET A 32 REMARK 465 ASP A 153 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 ALA B 61 165.96 178.39 REMARK 500 ASP B 120 69.82 65.27 REMARK 500 HIS A 87 79.05 -115.52 REMARK 500 ASP A 120 66.23 67.02 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 348 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 349 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A 350 DISTANCE = 6.38 ANGSTROMS DBREF 6P17 B 31 153 PDB 6P17 6P17 31 153 DBREF 6P17 A 31 153 PDB 6P17 6P17 31 153 SEQRES 1 B 123 SER MET HIS GLU TYR ASP VAL GLY LYS LEU LYS VAL GLU SEQRES 2 B 123 HIS PRO TRP LEU ARG ALA PRO ALA ASP GLY GLU LYS ASN SEQRES 3 B 123 ALA SER PHE TYR ALA PHE ILE HIS ASN ASN GLY ASP THR SEQRES 4 B 123 PRO ASP LYS LEU VAL ALA VAL LYS VAL GLU LYS PHE GLY SEQRES 5 B 123 SER ALA VAL ILE HIS GLY ASP ALA LYS ASN LEU ALA LEU SEQRES 6 B 123 GLU ALA PRO VAL LEU LEU PRO PRO LYS GLN LYS ILE THR SEQRES 7 B 123 LEU ALA PRO GLY GLY ALA TYR VAL ALA LEU LEU ASP ALA SEQRES 8 B 123 LYS LYS HIS LEU GLU VAL GLY TRP GLY LEU GLU MET THR SEQRES 9 B 123 LEU VAL PHE GLU LYS ALA GLY GLU VAL VAL ILE ASP ALA SEQRES 10 B 123 ALA ILE ASP ALA PRO ASP SEQRES 1 A 123 SER MET HIS GLU TYR ASP VAL GLY LYS LEU LYS VAL GLU SEQRES 2 A 123 HIS PRO TRP LEU ARG ALA PRO ALA ASP GLY GLU LYS ASN SEQRES 3 A 123 ALA SER PHE TYR ALA PHE ILE HIS ASN ASN GLY ASP THR SEQRES 4 A 123 PRO ASP LYS LEU VAL ALA VAL LYS VAL GLU LYS PHE GLY SEQRES 5 A 123 SER ALA VAL ILE HIS GLY ASP ALA LYS ASN LEU ALA LEU SEQRES 6 A 123 GLU ALA PRO VAL LEU LEU PRO PRO LYS GLN LYS ILE THR SEQRES 7 A 123 LEU ALA PRO GLY GLY ALA TYR VAL ALA LEU LEU ASP ALA SEQRES 8 A 123 LYS LYS HIS LEU GLU VAL GLY TRP GLY LEU GLU MET THR SEQRES 9 A 123 LEU VAL PHE GLU LYS ALA GLY GLU VAL VAL ILE ASP ALA SEQRES 10 A 123 ALA ILE ASP ALA PRO ASP FORMUL 3 HOH *271(H2 O) HELIX 1 AA1 ASP A 89 LEU A 93 5 5 SHEET 1 AA1 7 GLU B 34 VAL B 37 0 SHEET 2 AA1 7 LEU B 40 ARG B 48 -1 O VAL B 42 N TYR B 35 SHEET 3 AA1 7 ALA B 57 ASN B 65 -1 O TYR B 60 N TRP B 46 SHEET 4 AA1 7 GLY B 141 ASP B 150 0 SHEET 5 AA1 7 LEU B 131 PHE B 137 -1 N MET B 133 O ILE B 145 SHEET 6 AA1 7 ASP B 71 VAL B 78 -1 N LYS B 77 O THR B 134 SHEET 7 AA1 7 VAL B 99 LEU B 101 -1 O LEU B 101 N ASP B 71 SHEET 1 AA2 5 PHE B 81 HIS B 87 0 SHEET 2 AA2 5 TYR B 115 ALA B 121 -1 O ALA B 117 N VAL B 85 SHEET 3 AA2 5 ALA B 57 ASN B 65 -1 N ALA B 57 O LEU B 118 SHEET 4 AA2 5 LEU B 40 ARG B 48 -1 N TRP B 46 O TYR B 60 SHEET 5 AA2 5 GLN B 105 LEU B 109 0 SHEET 1 AA3 7 GLU A 34 VAL A 37 0 SHEET 2 AA3 7 LEU A 40 ARG A 48 -1 O VAL A 42 N TYR A 35 SHEET 3 AA3 7 ALA A 57 ASN A 65 -1 O HIS A 64 N LYS A 41 SHEET 4 AA3 7 GLY A 141 ASP A 150 0 SHEET 5 AA3 7 LEU A 131 PHE A 137 -1 N MET A 133 O ILE A 145 SHEET 6 AA3 7 ASP A 71 VAL A 78 -1 N LYS A 77 O THR A 134 SHEET 7 AA3 7 VAL A 99 LEU A 101 -1 O LEU A 101 N ASP A 71 SHEET 1 AA4 5 PHE A 81 HIS A 87 0 SHEET 2 AA4 5 TYR A 115 ALA A 121 -1 O ALA A 117 N VAL A 85 SHEET 3 AA4 5 ALA A 57 ASN A 65 -1 N ALA A 57 O LEU A 118 SHEET 4 AA4 5 LEU A 40 ARG A 48 -1 N LYS A 41 O HIS A 64 SHEET 5 AA4 5 GLN A 105 LEU A 109 0 CRYST1 47.642 60.579 85.100 90.00 90.00 90.00 P 21 21 21 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 0.020990 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016507 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011751 0.00000