HEADER LIPID BINDING PROTEIN 07-SEP-19 6KWJ TITLE A CRYSTAL STRUCTURE OF OSPA MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER SURFACE PROTEIN A; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: OSPA163; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORRELIA BURGDORFERI (STRAIN ATCC 35210 / B31 / SOURCE 3 CIP 102532 / DSM 4680); SOURCE 4 ORGANISM_TAXID: 224326; SOURCE 5 STRAIN: ATCC 35210 / B31 / CIP 102532 / DSM 4680; SOURCE 6 GENE: OSPA, BB_A15; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS OUTER SURFACE PROTEIN A, OSPA, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.KIYA,K.MAKABE REVDAT 3 21-FEB-24 6KWJ 1 JRNL REVDAT 2 22-NOV-23 6KWJ 1 REMARK REVDAT 1 09-SEP-20 6KWJ 0 JRNL AUTH M.KIYA,S.SHIGA,P.DING,S.KOIDE,K.MAKABE JRNL TITL BETA-STRAND-MEDIATED DOMAIN-SWAPPING IN THE ABSENCE OF JRNL TITL 2 HYDROPHOBIC CORE REPACKING. JRNL REF J.MOL.BIOL. V. 436 68405 2024 JRNL REFN ESSN 1089-8638 JRNL PMID 38104859 JRNL DOI 10.1016/J.JMB.2023.168405 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 22185 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1123 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 19.9000 - 3.8700 0.99 2743 135 0.1675 0.1944 REMARK 3 2 3.8700 - 3.0800 0.99 2660 132 0.1856 0.2113 REMARK 3 3 3.0800 - 2.6900 0.99 2643 133 0.2247 0.2549 REMARK 3 4 2.6900 - 2.4400 0.99 2618 138 0.2297 0.2906 REMARK 3 5 2.4400 - 2.2700 0.99 2631 144 0.2282 0.3120 REMARK 3 6 2.2700 - 2.1400 0.99 2584 149 0.2249 0.2976 REMARK 3 7 2.1400 - 2.0300 0.99 2588 149 0.2300 0.3073 REMARK 3 8 2.0300 - 1.9400 0.99 2595 143 0.2544 0.3121 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) : 0.259 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.494 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.09 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 : 0.006 1749 REMARK 3 ANGLE : 0.781 2358 REMARK 3 CHIRALITY : 0.054 300 REMARK 3 PLANARITY : 0.004 295 REMARK 3 DIHEDRAL : 20.353 645 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 6KWJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013540. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22185 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 19.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 11.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2G8C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26%PEG 400, 0.1M IMIDOZOLE, 16.1 REMARK 280 MG/ML, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 282K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 64.25050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.36700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 64.25050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.36700 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: 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 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 B 23 REMARK 465 SER B 24 REMARK 465 HIS B 25 REMARK 465 MET B 26 REMARK 465 LYS B 27 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 60 -11.31 66.63 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 B 550 DISTANCE = 6.82 ANGSTROMS DBREF 6KWJ B 27 266 UNP P0CL66 OSPA_BORBU 27 273 SEQADV 6KWJ GLY B 23 UNP P0CL66 EXPRESSION TAG SEQADV 6KWJ SER B 24 UNP P0CL66 EXPRESSION TAG SEQADV 6KWJ HIS B 25 UNP P0CL66 EXPRESSION TAG SEQADV 6KWJ MET B 26 UNP P0CL66 EXPRESSION TAG SEQADV 6KWJ SER B 37 UNP P0CL66 GLU 37 ENGINEERED MUTATION SEQADV 6KWJ SER B 45 UNP P0CL66 GLU 45 ENGINEERED MUTATION SEQADV 6KWJ SER B 46 UNP P0CL66 LYS 46 ENGINEERED MUTATION SEQADV 6KWJ ALA B 48 UNP P0CL66 LYS 48 ENGINEERED MUTATION SEQADV 6KWJ ALA B 60 UNP P0CL66 LYS 60 ENGINEERED MUTATION SEQADV 6KWJ SER B 64 UNP P0CL66 LYS 64 ENGINEERED MUTATION SEQADV 6KWJ ALA B 83 UNP P0CL66 LYS 83 ENGINEERED MUTATION SEQADV 6KWJ SER B 104 UNP P0CL66 GLU 104 ENGINEERED MUTATION SEQADV 6KWJ SER B 107 UNP P0CL66 LYS 107 ENGINEERED MUTATION SEQADV 6KWJ GLY B 117 UNP P0CL66 LYS 117 ENGINEERED MUTATION SEQADV 6KWJ GLY B 118 UNP P0CL66 ASP 118 ENGINEERED MUTATION SEQADV 6KWJ B UNP P0CL66 LYS 119 DELETION SEQADV 6KWJ GLY B 125 UNP P0CL66 PHE 126 ENGINEERED MUTATION SEQADV 6KWJ GLY B 126 UNP P0CL66 ASN 127 ENGINEERED MUTATION SEQADV 6KWJ B UNP P0CL66 GLY 130 DELETION SEQADV 6KWJ B UNP P0CL66 GLU 131 DELETION SEQADV 6KWJ B UNP P0CL66 VAL 132 DELETION SEQADV 6KWJ B UNP P0CL66 SER 133 DELETION SEQADV 6KWJ B UNP P0CL66 GLU 134 DELETION SEQADV 6KWJ B UNP P0CL66 LYS 135 DELETION SEQADV 6KWJ SER B 232 UNP P0CL66 LYS 239 ENGINEERED MUTATION SEQADV 6KWJ SER B 233 UNP P0CL66 GLU 240 ENGINEERED MUTATION SEQADV 6KWJ SER B 247 UNP P0CL66 LYS 254 ENGINEERED MUTATION SEQRES 1 B 244 GLY SER HIS MET LYS ASN SER VAL SER VAL ASP LEU PRO SEQRES 2 B 244 GLY SER MET LYS VAL LEU VAL SER LYS SER SER ASN ALA SEQRES 3 B 244 ASP GLY LYS TYR ASP LEU ILE ALA THR VAL ASP ALA LEU SEQRES 4 B 244 GLU LEU SER GLY THR SER ASP LYS ASN ASN GLY SER GLY SEQRES 5 B 244 VAL LEU GLU GLY VAL LYS ALA ASP ALA SER LYS VAL LYS SEQRES 6 B 244 LEU THR ILE SER ASP ASP LEU GLY GLN THR THR LEU GLU SEQRES 7 B 244 VAL PHE LYS SER ASP GLY SER THR LEU VAL SER LYS LYS SEQRES 8 B 244 VAL THR SER GLY GLY SER SER THR GLU GLU LYS GLY GLY SEQRES 9 B 244 GLU LYS ILE ILE THR ARG ALA ASP GLY THR ARG LEU GLU SEQRES 10 B 244 TYR THR GLY ILE LYS SER ASP GLY SER GLY LYS ALA LYS SEQRES 11 B 244 GLU VAL LEU LYS GLY TYR VAL LEU GLU GLY THR LEU THR SEQRES 12 B 244 ALA GLU LYS THR THR LEU VAL VAL LYS GLU GLY THR VAL SEQRES 13 B 244 THR LEU SER LYS ASN ILE SER LYS SER GLY GLU VAL SER SEQRES 14 B 244 VAL GLU LEU ASN ASP THR ASP SER SER ALA ALA THR LYS SEQRES 15 B 244 LYS THR ALA ALA TRP ASN SER GLY THR SER THR LEU THR SEQRES 16 B 244 ILE THR VAL ASN SER LYS LYS THR LYS ASP LEU VAL PHE SEQRES 17 B 244 THR SER SER ASN THR ILE THR VAL GLN GLN TYR ASP SER SEQRES 18 B 244 ASN GLY THR SER LEU GLU GLY SER ALA VAL GLU ILE THR SEQRES 19 B 244 LYS LEU ASP GLU ILE LYS ASN ALA LEU LYS FORMUL 2 HOH *250(H2 O) HELIX 1 AA1 PRO B 35 SER B 37 5 3 HELIX 2 AA2 LYS B 257 LEU B 265 1 9 SHEET 1 AA1 4 SER B 29 ASP B 33 0 SHEET 2 AA1 4 LYS B 39 SER B 43 -1 O VAL B 40 N VAL B 32 SHEET 3 AA1 4 TYR B 52 VAL B 58 -1 O ILE B 55 N LEU B 41 SHEET 4 AA1 4 LEU B 61 SER B 67 -1 O LEU B 61 N VAL B 58 SHEET 1 AA2 5 GLY B 74 VAL B 79 0 SHEET 2 AA2 5 LYS B 85 ILE B 90 -1 O VAL B 86 N GLY B 78 SHEET 3 AA2 5 GLN B 96 PHE B 102 -1 O GLU B 100 N LYS B 87 SHEET 4 AA2 5 LEU B 109 SER B 116 -1 O VAL B 110 N VAL B 101 SHEET 5 AA2 5 SER B 119 LYS B 124 -1 O GLU B 123 N LYS B 112 SHEET 1 AA3 7 GLY B 126 THR B 131 0 SHEET 2 AA3 7 ARG B 137 ILE B 143 -1 O LEU B 138 N ILE B 130 SHEET 3 AA3 7 GLY B 149 VAL B 154 -1 O LYS B 152 N GLU B 139 SHEET 4 AA3 7 VAL B 159 THR B 165 -1 O LEU B 164 N GLY B 149 SHEET 5 AA3 7 LYS B 168 GLU B 175 -1 O VAL B 172 N GLU B 161 SHEET 6 AA3 7 VAL B 178 ILE B 184 -1 O LEU B 180 N VAL B 173 SHEET 7 AA3 7 VAL B 190 ASP B 196 -1 O SER B 191 N ASN B 183 SHEET 1 AA4 5 LYS B 205 ASN B 210 0 SHEET 2 AA4 5 THR B 215 VAL B 220 -1 O THR B 219 N THR B 206 SHEET 3 AA4 5 LYS B 223 PHE B 230 -1 O LEU B 228 N LEU B 216 SHEET 4 AA4 5 ILE B 236 GLN B 240 -1 O GLN B 239 N ASP B 227 SHEET 5 AA4 5 VAL B 253 GLU B 254 -1 O VAL B 253 N VAL B 238 CRYST1 128.501 32.734 72.247 90.00 100.28 90.00 C 1 2 1 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 0.007782 0.000000 0.001411 0.00000 SCALE2 0.000000 0.030549 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014067 0.00000