HEADER LIGASE 14-MAR-17 5NFK TITLE CRYSTAL STRUCTURE OF YRBA FROM SINORHIZOBIUM MELILOTI IN COMPLEX WITH TITLE 2 NICKEL. COMPND MOL_ID: 1; COMPND 2 MOLECULE: YRBA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SINORHIZOBIUM MELILOTI (STRAIN SM2011 / RM2011 SOURCE 3 / 2011); SOURCE 4 ORGANISM_TAXID: 1286640; SOURCE 5 GENE: SM2011_C00487; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BOLA, YRBA, HISTIDYL LIGATION, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR T.RORET,C.DIDIERJEAN REVDAT 3 08-MAY-24 5NFK 1 REMARK REVDAT 2 02-DEC-20 5NFK 1 COMPND JRNL LINK REVDAT 1 10-OCT-18 5NFK 0 JRNL AUTH T.RORET,G.ALLOING,J.M.GIRARDET,T.PERROT,T.DHALLEINE, JRNL AUTH 2 J.COUTURIER,P.FRENDO,C.DIDIERJEAN,N.ROUHIER JRNL TITL SINORHIZOBIUM MELILOTI YRBA BINDS DIVALENT METAL CATIONS JRNL TITL 2 USING TWO CONSERVED HISTIDINES. JRNL REF BIOSCI.REP. V. 40 2020 JRNL REFN ISSN 0144-8463 JRNL PMID 32970113 JRNL DOI 10.1042/BSR20202956 REMARK 2 REMARK 2 RESOLUTION. 0.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 0.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 35335 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.102 REMARK 3 R VALUE (WORKING SET) : 0.101 REMARK 3 FREE R VALUE : 0.113 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1771 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 31.4326 - 2.3040 1.00 2854 154 0.1242 0.1231 REMARK 3 2 2.3040 - 1.8288 1.00 2720 135 0.0969 0.1083 REMARK 3 3 1.8288 - 1.5977 1.00 2682 136 0.0927 0.1046 REMARK 3 4 1.5977 - 1.4516 1.00 2660 148 0.0880 0.0976 REMARK 3 5 1.4516 - 1.3476 1.00 2659 140 0.0820 0.0992 REMARK 3 6 1.3476 - 1.2681 1.00 2668 128 0.0758 0.0956 REMARK 3 7 1.2681 - 1.2046 1.00 2633 140 0.0765 0.0902 REMARK 3 8 1.2046 - 1.1522 1.00 2641 144 0.0802 0.0932 REMARK 3 9 1.1522 - 1.1078 1.00 2609 142 0.0782 0.1261 REMARK 3 10 1.1078 - 1.0696 1.00 2612 144 0.0878 0.0970 REMARK 3 11 1.0696 - 1.0361 0.99 2589 145 0.1138 0.1274 REMARK 3 12 1.0361 - 1.0065 0.90 2349 120 0.1417 0.1765 REMARK 3 13 1.0065 - 0.9800 0.72 1888 95 0.1972 0.2287 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) : 0.040 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 9.020 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 : 0.009 634 REMARK 3 ANGLE : 1.372 866 REMARK 3 CHIRALITY : 0.087 92 REMARK 3 PLANARITY : 0.006 121 REMARK 3 DIHEDRAL : 12.042 248 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 5NFK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200004026. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-14 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 : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : REMARK 200 1.485952,1.486573,1.482608,0.979993 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35397 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.980 REMARK 200 RESOLUTION RANGE LOW (A) : 31.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.35900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M LITHIUM SULFATE 0.01 M NICKEL REMARK 280 CHLORIDE 0.1 M TRIS-HCL, PH 8.5, MICROBATCH, TEMPERATURE 277K 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 15.44350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.41650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.95850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.41650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.44350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.95850 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: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 MET A 3 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 ASP A 31 -60.89 -136.24 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 310 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A 311 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A 312 DISTANCE = 6.57 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 LI A 101 LI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 25 OD1 REMARK 620 2 LEU A 26 O 101.3 REMARK 620 3 ASP A 29 OD1 106.2 95.3 REMARK 620 4 HIS A 32 O 108.8 122.7 120.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 100 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 32 NE2 REMARK 620 2 HIS A 67 NE2 93.6 REMARK 620 3 HOH A 205 O 91.6 173.6 REMARK 620 4 HOH A 213 O 91.3 95.9 87.7 REMARK 620 5 HOH A 266 O 94.2 93.0 82.9 169.2 REMARK 620 6 HOH A 267 O 171.6 93.5 81.5 83.7 89.7 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 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LI A 101 DBREF 5NFK A 3 77 UNP M4MWA0 M4MWA0_SINM2 3 77 SEQRES 1 A 75 MET ALA PRO GLY ASP ILE GLU ASP MET ILE LYS ALA GLY SEQRES 2 A 75 ILE PRO GLY ALA ARG VAL THR ILE ARG ASP LEU ALA GLY SEQRES 3 A 75 ASP GLY ASP HIS TYR ALA ALA GLU VAL VAL ALA GLU ALA SEQRES 4 A 75 PHE ARG GLY LYS THR ARG VAL GLN GLN HIS GLN MET VAL SEQRES 5 A 75 TYR ASN ALA LEU LYS GLY ASN MET GLY GLY ILE LEU HIS SEQRES 6 A 75 ALA LEU ALA LEU GLN THR SER ALA PRO GLU HET NI A 100 1 HET LI A 101 1 HETNAM NI NICKEL (II) ION HETNAM LI LITHIUM ION FORMUL 2 NI NI 2+ FORMUL 3 LI LI 1+ FORMUL 4 HOH *112(H2 O) HELIX 1 AA1 GLY A 6 ILE A 16 1 11 HELIX 2 AA2 ALA A 27 ASP A 29 5 3 HELIX 3 AA3 GLU A 40 ARG A 43 5 4 HELIX 4 AA4 THR A 46 LYS A 59 1 14 HELIX 5 AA5 GLY A 64 ALA A 68 1 5 SHEET 1 AA1 3 ARG A 20 ASP A 25 0 SHEET 2 AA1 3 TYR A 33 VAL A 38 -1 O VAL A 38 N ARG A 20 SHEET 3 AA1 3 LEU A 69 SER A 74 1 O ALA A 70 N ALA A 35 LINK OD1 ASP A 25 LI LI A 101 1555 1555 1.93 LINK O LEU A 26 LI LI A 101 1555 1555 1.96 LINK OD1 ASP A 29 LI LI A 101 1555 1555 1.94 LINK NE2 HIS A 32 NI NI A 100 1555 1555 2.07 LINK O HIS A 32 LI LI A 101 1555 1555 1.90 LINK NE2 HIS A 67 NI NI A 100 1555 1555 2.07 LINK NI NI A 100 O HOH A 205 1555 1555 2.09 LINK NI NI A 100 O HOH A 213 1555 1555 2.09 LINK NI NI A 100 O HOH A 266 1555 1555 2.10 LINK NI NI A 100 O HOH A 267 1555 1555 2.11 SITE 1 AC1 6 HIS A 32 HIS A 67 HOH A 205 HOH A 213 SITE 2 AC1 6 HOH A 266 HOH A 267 SITE 1 AC2 4 ASP A 25 LEU A 26 ASP A 29 HIS A 32 CRYST1 30.887 31.917 62.833 90.00 90.00 90.00 P 21 21 21 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 0.032377 0.000000 0.000000 0.00000 SCALE2 0.000000 0.031331 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015915 0.00000