HEADER METAL BINDING PROTEIN 01-DEC-17 6F5N TITLE NICKEL-BOUND CRYSTAL STRUCTURE OF A GB1 VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICKEL-BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS; SOURCE 3 ORGANISM_TAXID: 1301; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NICKEL, GB1, PROTEIN SELF-ASSEMBLY, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR U.ROTHLISBERGER,E.BOZKURT,R.HOVIUS,M.A.S.PEREZ,N.J.BROWNING REVDAT 2 17-JAN-24 6F5N 1 LINK REVDAT 1 12-DEC-18 6F5N 0 JRNL AUTH E.BOZKURT,R.HOVIUS,N.J.BROWNING,M.A.S.PEREZ,U.ROTHLISBERGER JRNL TITL NICKEL-MEDIATED SELF-ASSEMBLY OF AN ULTRASTABLE GB1 VARIANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.2 REMARK 3 NUMBER OF REFLECTIONS : 9326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.267 REMARK 3 R VALUE (WORKING SET) : 0.257 REMARK 3 FREE R VALUE : 0.356 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.840 REMARK 3 FREE R VALUE TEST SET COUNT : 918 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 46.7131 - 4.2081 1.00 1501 172 0.2350 0.2818 REMARK 3 2 4.2081 - 3.3404 0.98 1502 134 0.2174 0.3864 REMARK 3 3 3.3404 - 2.9182 0.88 1355 145 0.2596 0.3588 REMARK 3 4 2.9182 - 2.6514 0.79 1181 142 0.2816 0.3765 REMARK 3 5 2.6514 - 2.4614 0.70 1047 146 0.2874 0.4147 REMARK 3 6 2.4614 - 2.3163 0.64 966 97 0.3079 0.3905 REMARK 3 7 2.3163 - 2.2003 0.56 856 82 0.3287 0.4158 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) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.040 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) : 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 : 0.013 934 REMARK 3 ANGLE : 1.238 1256 REMARK 3 CHIRALITY : 0.062 139 REMARK 3 PLANARITY : 0.006 162 REMARK 3 DIHEDRAL : 18.516 536 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 6F5N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007781. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-17 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADDREF REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49277 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 46.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.350 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: 1IGD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NICKEL (II) CHLORIDE REMARK 280 HEXAHYDRATE, 0.1 M TRIS, 20 % W/V PEG 4000, PH 8.5., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 13.34000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.86450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.66400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.86450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.34000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.66400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 B 112 O HOH B 115 1.96 REMARK 500 OD2 ASP B 27 O HOH B 101 2.01 REMARK 500 O HIS A 55 O HOH A 201 2.04 REMARK 500 O HOH B 101 O HOH B 122 2.06 REMARK 500 O THR B 16 O HOH B 102 2.11 REMARK 500 O HOH A 202 O HOH A 211 2.13 REMARK 500 O HOH A 221 O HOH B 128 2.14 REMARK 500 OE1 GLU A 52 O HOH A 202 2.14 REMARK 500 O GLY B 14 NZ LYS B 18 2.17 REMARK 500 OXT GLU B 61 O HOH B 103 2.17 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 15 -86.96 -60.43 REMARK 500 LYS A 15 -82.70 -64.80 REMARK 500 GLU B 24 69.72 -119.52 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 NI A 101 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 28 NE2 REMARK 620 2 GLU A 32 OE1 77.4 REMARK 620 3 HIS B 28 NE2 100.9 99.1 REMARK 620 4 GLU B 32 OE1 105.3 176.0 83.5 REMARK 620 5 HOH B 112 O 151.9 104.4 106.5 71.8 REMARK 620 6 HOH B 115 O 101.3 97.4 154.8 79.2 50.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5OFS RELATED DB: PDB REMARK 900 RELATED ID: 5O94 RELATED DB: PDB DBREF 6F5N A 6 61 PDB 6F5N 6F5N 6 61 DBREF 6F5N B 6 61 PDB 6F5N 6F5N 6 61 SEQRES 1 A 56 MET GLN PHE LYS LEU ILE LEU ASN GLY LYS THR LEU LYS SEQRES 2 A 56 GLY VAL ILE THR ILE GLU ALA VAL ASP HIS ALA GLU ALA SEQRES 3 A 56 GLU LYS PHE PHE LYS GLN TYR ALA ASN ASP ASN GLY VAL SEQRES 4 A 56 ASP GLY GLU TRP THR TYR ASP GLU ALA THR HIS THR PHE SEQRES 5 A 56 THR VAL THR GLU SEQRES 1 B 56 MET GLN PHE LYS LEU ILE LEU ASN GLY LYS THR LEU LYS SEQRES 2 B 56 GLY VAL ILE THR ILE GLU ALA VAL ASP HIS ALA GLU ALA SEQRES 3 B 56 GLU LYS PHE PHE LYS GLN TYR ALA ASN ASP ASN GLY VAL SEQRES 4 B 56 ASP GLY GLU TRP THR TYR ASP GLU ALA THR HIS THR PHE SEQRES 5 B 56 THR VAL THR GLU HET NI A 101 1 HETNAM NI NICKEL (II) ION FORMUL 3 NI NI 2+ FORMUL 4 HOH *64(H2 O) HELIX 1 AA1 ASP A 27 GLY A 43 1 17 HELIX 2 AA2 ASP B 27 ASN B 42 1 16 SHEET 1 AA1 4 LYS A 18 GLU A 24 0 SHEET 2 AA1 4 GLN A 7 ASN A 13 -1 N LEU A 10 O ILE A 21 SHEET 3 AA1 4 THR A 56 THR A 60 1 O PHE A 57 N LYS A 9 SHEET 4 AA1 4 GLU A 47 ASP A 51 -1 N ASP A 51 O THR A 56 SHEET 1 AA2 4 LYS B 18 GLU B 24 0 SHEET 2 AA2 4 GLN B 7 ASN B 13 -1 N PHE B 8 O ILE B 23 SHEET 3 AA2 4 THR B 56 THR B 60 1 O PHE B 57 N LYS B 9 SHEET 4 AA2 4 GLU B 47 ASP B 51 -1 N ASP B 51 O THR B 56 LINK NE2 HIS A 28 NI NI A 101 1555 1555 2.05 LINK OE1 GLU A 32 NI NI A 101 1555 1555 1.82 LINK NI NI A 101 NE2 HIS B 28 1555 1555 2.07 LINK NI NI A 101 OE1 GLU B 32 1555 1555 2.13 LINK NI NI A 101 O HOH B 112 1555 1555 2.33 LINK NI NI A 101 O HOH B 115 1555 1555 2.27 SITE 1 AC1 6 HIS A 28 GLU A 32 HIS B 28 GLU B 32 SITE 2 AC1 6 HOH B 112 HOH B 115 CRYST1 26.680 59.328 75.729 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 0.037481 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016855 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013205 0.00000