HEADER LIPID BINDING PROTEIN 08-SEP-19 6KWU TITLE A CRYSTAL STRUCTURE OF OSPA MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER SURFACE PROTEIN A; COMPND 3 CHAIN: O; COMPND 4 SYNONYM: OSPA149; 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 6KWU 1 JRNL REVDAT 2 22-NOV-23 6KWU 1 REMARK REVDAT 1 09-SEP-20 6KWU 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. 1.43 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 42481 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2139 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 19.7600 - 3.5200 0.99 2754 165 0.1718 0.1982 REMARK 3 2 3.5200 - 2.8000 1.00 2711 140 0.1855 0.2328 REMARK 3 3 2.8000 - 2.4400 0.99 2707 144 0.1965 0.2060 REMARK 3 4 2.4400 - 2.2200 1.00 2720 128 0.1854 0.2209 REMARK 3 5 2.2200 - 2.0600 1.00 2685 152 0.1749 0.2089 REMARK 3 6 2.0600 - 1.9400 0.99 2677 142 0.1792 0.2215 REMARK 3 7 1.9400 - 1.8400 0.99 2714 127 0.1850 0.2162 REMARK 3 8 1.8400 - 1.7600 0.99 2710 135 0.1826 0.2428 REMARK 3 9 1.7600 - 1.7000 0.99 2675 145 0.1907 0.2208 REMARK 3 10 1.7000 - 1.6400 0.99 2649 152 0.1921 0.2236 REMARK 3 11 1.6400 - 1.5900 0.99 2648 160 0.1966 0.2457 REMARK 3 12 1.5900 - 1.5400 0.99 2707 136 0.1966 0.2313 REMARK 3 13 1.5400 - 1.5000 0.99 2639 146 0.2038 0.2148 REMARK 3 14 1.5000 - 1.4600 1.00 2714 133 0.2173 0.2250 REMARK 3 15 1.4600 - 1.4300 0.99 2632 134 0.2363 0.2755 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) : 0.137 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.566 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.97 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 : 0.004 1795 REMARK 3 ANGLE : 0.726 2420 REMARK 3 CHIRALITY : 0.077 308 REMARK 3 PLANARITY : 0.003 302 REMARK 3 DIHEDRAL : 3.316 1075 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 6KWU 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_1300013776. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-07 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 : APS REMARK 200 BEAMLINE : 23-ID-D 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 : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42482 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.270 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 (%): 45.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 36% PEG 400, 0.1M TRIS PH 7.0, 0.05M REMARK 280 MGSO4, 24.6 MG/ML (12.3 MG/ML 2UL:1UL), VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 282K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 27.19400 REMARK 290 SMTRY3 2 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: O 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 O 23 REMARK 465 SER O 24 REMARK 465 HIS O 25 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 ASN O 28 55.53 -112.64 REMARK 500 ASP O 59 -120.85 54.68 REMARK 500 ALA O 83 -0.28 80.77 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 O 661 DISTANCE = 6.77 ANGSTROMS DBREF 6KWU O 27 270 UNP P0CL66 OSPA_BORBU 27 273 SEQADV 6KWU GLY O 23 UNP P0CL66 EXPRESSION TAG SEQADV 6KWU SER O 24 UNP P0CL66 EXPRESSION TAG SEQADV 6KWU HIS O 25 UNP P0CL66 EXPRESSION TAG SEQADV 6KWU MET O 26 UNP P0CL66 EXPRESSION TAG SEQADV 6KWU SER O 37 UNP P0CL66 GLU 37 ENGINEERED MUTATION SEQADV 6KWU SER O 45 UNP P0CL66 GLU 45 ENGINEERED MUTATION SEQADV 6KWU SER O 46 UNP P0CL66 LYS 46 ENGINEERED MUTATION SEQADV 6KWU ALA O 48 UNP P0CL66 LYS 48 ENGINEERED MUTATION SEQADV 6KWU ALA O 60 UNP P0CL66 LYS 60 ENGINEERED MUTATION SEQADV 6KWU SER O 64 UNP P0CL66 LYS 64 ENGINEERED MUTATION SEQADV 6KWU ALA O 83 UNP P0CL66 LYS 83 ENGINEERED MUTATION SEQADV 6KWU SER O 104 UNP P0CL66 GLU 104 ENGINEERED MUTATION SEQADV 6KWU SER O 107 UNP P0CL66 LYS 107 ENGINEERED MUTATION SEQADV 6KWU GLY O 117 UNP P0CL66 LYS 117 ENGINEERED MUTATION SEQADV 6KWU GLY O 118 UNP P0CL66 ASP 118 ENGINEERED MUTATION SEQADV 6KWU O UNP P0CL66 LYS 119 DELETION SEQADV 6KWU O UNP P0CL66 PHE 126 DELETION SEQADV 6KWU O UNP P0CL66 ASN 127 DELETION SEQADV 6KWU SER O 125 UNP P0CL66 GLU 128 ENGINEERED MUTATION SEQADV 6KWU SER O 126 UNP P0CL66 LYS 129 ENGINEERED MUTATION SEQADV 6KWU GLY O 128 UNP P0CL66 GLU 131 ENGINEERED MUTATION SEQADV 6KWU SER O 129 UNP P0CL66 VAL 132 ENGINEERED MUTATION SEQADV 6KWU SER O 236 UNP P0CL66 LYS 239 ENGINEERED MUTATION SEQADV 6KWU SER O 237 UNP P0CL66 GLU 240 ENGINEERED MUTATION SEQADV 6KWU SER O 251 UNP P0CL66 LYS 254 ENGINEERED MUTATION SEQRES 1 O 248 GLY SER HIS MET LYS ASN SER VAL SER VAL ASP LEU PRO SEQRES 2 O 248 GLY SER MET LYS VAL LEU VAL SER LYS SER SER ASN ALA SEQRES 3 O 248 ASP GLY LYS TYR ASP LEU ILE ALA THR VAL ASP ALA LEU SEQRES 4 O 248 GLU LEU SER GLY THR SER ASP LYS ASN ASN GLY SER GLY SEQRES 5 O 248 VAL LEU GLU GLY VAL LYS ALA ASP ALA SER LYS VAL LYS SEQRES 6 O 248 LEU THR ILE SER ASP ASP LEU GLY GLN THR THR LEU GLU SEQRES 7 O 248 VAL PHE LYS SER ASP GLY SER THR LEU VAL SER LYS LYS SEQRES 8 O 248 VAL THR SER GLY GLY SER SER THR GLU GLU LYS SER SER SEQRES 9 O 248 GLY GLY SER SER GLU LYS ILE ILE THR ARG ALA ASP GLY SEQRES 10 O 248 THR ARG LEU GLU TYR THR GLY ILE LYS SER ASP GLY SER SEQRES 11 O 248 GLY LYS ALA LYS GLU VAL LEU LYS GLY TYR VAL LEU GLU SEQRES 12 O 248 GLY THR LEU THR ALA GLU LYS THR THR LEU VAL VAL LYS SEQRES 13 O 248 GLU GLY THR VAL THR LEU SER LYS ASN ILE SER LYS SER SEQRES 14 O 248 GLY GLU VAL SER VAL GLU LEU ASN ASP THR ASP SER SER SEQRES 15 O 248 ALA ALA THR LYS LYS THR ALA ALA TRP ASN SER GLY THR SEQRES 16 O 248 SER THR LEU THR ILE THR VAL ASN SER LYS LYS THR LYS SEQRES 17 O 248 ASP LEU VAL PHE THR SER SER ASN THR ILE THR VAL GLN SEQRES 18 O 248 GLN TYR ASP SER ASN GLY THR SER LEU GLU GLY SER ALA SEQRES 19 O 248 VAL GLU ILE THR LYS LEU ASP GLU ILE LYS ASN ALA LEU SEQRES 20 O 248 LYS FORMUL 2 HOH *361(H2 O) HELIX 1 AA1 LYS O 261 LEU O 269 1 9 SHEET 1 AA1 4 SER O 29 LEU O 34 0 SHEET 2 AA1 4 MET O 38 SER O 43 -1 O MET O 38 N LEU O 34 SHEET 3 AA1 4 TYR O 52 VAL O 58 -1 O ILE O 55 N LEU O 41 SHEET 4 AA1 4 LEU O 61 SER O 67 -1 O LEU O 63 N ALA O 56 SHEET 1 AA212 GLY O 74 VAL O 79 0 SHEET 2 AA212 LYS O 85 ILE O 90 -1 O ILE O 90 N GLY O 74 SHEET 3 AA212 GLN O 96 PHE O 102 -1 O PHE O 102 N LYS O 85 SHEET 4 AA212 LEU O 109 SER O 116 -1 O VAL O 110 N VAL O 101 SHEET 5 AA212 SER O 119 SER O 126 -1 O GLU O 123 N LYS O 112 SHEET 6 AA212 SER O 129 THR O 135 -1 O THR O 135 N SER O 120 SHEET 7 AA212 ARG O 141 ILE O 147 -1 O LEU O 142 N ILE O 134 SHEET 8 AA212 GLY O 153 LEU O 159 -1 O LYS O 156 N GLU O 143 SHEET 9 AA212 TYR O 162 LEU O 168 -1 O LEU O 164 N GLU O 157 SHEET 10 AA212 LYS O 172 GLU O 179 -1 O THR O 174 N THR O 167 SHEET 11 AA212 VAL O 182 SER O 189 -1 O LYS O 186 N LEU O 175 SHEET 12 AA212 VAL O 194 ASP O 200 -1 O SER O 195 N ASN O 187 SHEET 1 AA3 5 LYS O 209 ASN O 214 0 SHEET 2 AA3 5 THR O 219 VAL O 224 -1 O THR O 223 N THR O 210 SHEET 3 AA3 5 LYS O 227 PHE O 234 -1 O LEU O 232 N LEU O 220 SHEET 4 AA3 5 ILE O 240 GLN O 244 -1 O GLN O 243 N ASP O 231 SHEET 5 AA3 5 VAL O 257 GLU O 258 -1 O VAL O 257 N VAL O 242 CRYST1 33.081 54.388 66.236 90.00 100.18 90.00 P 1 21 1 2 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 0.030229 0.000000 0.005429 0.00000 SCALE2 0.000000 0.018386 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015339 0.00000