HEADER LIPID BINDING PROTEIN 08-JAN-19 6J48 TITLE GLYCINE MUTATION ON SINGLE LAYER BETA-SHEET OF OSPASM1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER SURFACE PROTEIN A; COMPND 3 CHAIN: O; COMPND 4 ENGINEERED: YES; COMPND 5 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; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-SHEET, DE NOVO PROTEIN, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.MAKABE,Y.HORI REVDAT 3 22-NOV-23 6J48 1 REMARK REVDAT 2 17-APR-19 6J48 1 JRNL REVDAT 1 06-MAR-19 6J48 0 SPRSDE 06-MAR-19 6J48 5B11 JRNL AUTH Y.HORI,H.FUJIWARA,W.FUJIWARA,K.MAKABE JRNL TITL GRAFTING A SHORT CHAMELEON SEQUENCE FROM ALPHA B CRYSTALLIN JRNL TITL 2 INTO A BETA-SHEET SCAFFOLD PROTEIN. JRNL REF PROTEINS V. 87 416 2019 JRNL REFN ESSN 1097-0134 JRNL PMID 30684364 JRNL DOI 10.1002/PROT.25663 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 70769 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.134 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 3575 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 31.4317 - 3.5555 0.95 2569 128 0.1781 0.1865 REMARK 3 2 3.5555 - 2.8227 0.99 2638 132 0.1560 0.2016 REMARK 3 3 2.8227 - 2.4660 0.98 2590 144 0.1455 0.1727 REMARK 3 4 2.4660 - 2.2406 0.99 2600 151 0.1322 0.1427 REMARK 3 5 2.2406 - 2.0801 0.99 2577 156 0.1176 0.1336 REMARK 3 6 2.0801 - 1.9574 1.00 2632 136 0.1134 0.1330 REMARK 3 7 1.9574 - 1.8594 1.00 2634 135 0.1127 0.1274 REMARK 3 8 1.8594 - 1.7785 1.00 2628 143 0.1186 0.1522 REMARK 3 9 1.7785 - 1.7100 1.00 2586 162 0.1168 0.1416 REMARK 3 10 1.7100 - 1.6510 1.00 2593 127 0.1150 0.1617 REMARK 3 11 1.6510 - 1.5994 0.99 2632 140 0.1110 0.1147 REMARK 3 12 1.5994 - 1.5537 0.99 2588 138 0.1051 0.1362 REMARK 3 13 1.5537 - 1.5128 0.99 2604 141 0.1044 0.1357 REMARK 3 14 1.5128 - 1.4759 0.99 2588 147 0.1055 0.1442 REMARK 3 15 1.4759 - 1.4423 0.99 2574 148 0.1059 0.1176 REMARK 3 16 1.4423 - 1.4116 0.99 2598 131 0.1047 0.1281 REMARK 3 17 1.4116 - 1.3834 0.99 2530 153 0.1020 0.1507 REMARK 3 18 1.3834 - 1.3573 0.98 2595 133 0.1049 0.1394 REMARK 3 19 1.3573 - 1.3330 0.98 2588 132 0.1028 0.1232 REMARK 3 20 1.3330 - 1.3104 0.98 2617 112 0.1040 0.1529 REMARK 3 21 1.3104 - 1.2893 0.98 2530 150 0.1085 0.1402 REMARK 3 22 1.2893 - 1.2695 0.98 2529 138 0.1091 0.1422 REMARK 3 23 1.2695 - 1.2508 0.98 2592 132 0.1087 0.1401 REMARK 3 24 1.2508 - 1.2332 0.97 2574 106 0.1131 0.1540 REMARK 3 25 1.2332 - 1.2165 0.98 2527 135 0.1190 0.1558 REMARK 3 26 1.2165 - 1.2007 0.95 2481 125 0.1275 0.1583 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.030 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 : 0.007 1931 REMARK 3 ANGLE : 0.931 2611 REMARK 3 CHIRALITY : 0.081 325 REMARK 3 PLANARITY : 0.005 331 REMARK 3 DIHEDRAL : 12.637 729 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 6J48 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1300010433. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 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) : 1.000 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70798 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04700 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) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.15600 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: NULL REMARK 200 STARTING MODEL: 2G8C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 38% PEG 400, 0.1 M TRIS PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 27.22300 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 465 MET O 26 REMARK 465 LYS O 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 ASP O 59 -122.14 53.71 REMARK 500 ALA O 60 -6.41 75.39 REMARK 500 ALA O 83 -3.39 82.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 O 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 O 302 DBREF 6J48 O 27 273 UNP P0CL66 OSPA_BORBU 27 273 SEQADV 6J48 GLY O 23 UNP P0CL66 EXPRESSION TAG SEQADV 6J48 SER O 24 UNP P0CL66 EXPRESSION TAG SEQADV 6J48 HIS O 25 UNP P0CL66 EXPRESSION TAG SEQADV 6J48 MET O 26 UNP P0CL66 EXPRESSION TAG SEQADV 6J48 SER O 37 UNP P0CL66 GLU 37 ENGINEERED MUTATION SEQADV 6J48 SER O 45 UNP P0CL66 GLU 45 ENGINEERED MUTATION SEQADV 6J48 SER O 46 UNP P0CL66 LYS 46 ENGINEERED MUTATION SEQADV 6J48 ALA O 48 UNP P0CL66 LYS 48 ENGINEERED MUTATION SEQADV 6J48 ALA O 60 UNP P0CL66 LYS 60 ENGINEERED MUTATION SEQADV 6J48 SER O 64 UNP P0CL66 LYS 64 ENGINEERED MUTATION SEQADV 6J48 ALA O 83 UNP P0CL66 LYS 83 ENGINEERED MUTATION SEQADV 6J48 SER O 104 UNP P0CL66 GLU 104 ENGINEERED MUTATION SEQADV 6J48 SER O 107 UNP P0CL66 LYS 107 ENGINEERED MUTATION SEQADV 6J48 GLY O 122 UNP P0CL66 THR 122 ENGINEERED MUTATION SEQADV 6J48 ALA O 196 UNP P0CL66 GLU 196 ENGINEERED MUTATION SEQADV 6J48 SER O 239 UNP P0CL66 LYS 239 ENGINEERED MUTATION SEQADV 6J48 SER O 240 UNP P0CL66 GLU 240 ENGINEERED MUTATION SEQADV 6J48 SER O 254 UNP P0CL66 LYS 254 ENGINEERED MUTATION SEQRES 1 O 251 GLY SER HIS MET LYS ASN SER VAL SER VAL ASP LEU PRO SEQRES 2 O 251 GLY SER MET LYS VAL LEU VAL SER LYS SER SER ASN ALA SEQRES 3 O 251 ASP GLY LYS TYR ASP LEU ILE ALA THR VAL ASP ALA LEU SEQRES 4 O 251 GLU LEU SER GLY THR SER ASP LYS ASN ASN GLY SER GLY SEQRES 5 O 251 VAL LEU GLU GLY VAL LYS ALA ASP ALA SER LYS VAL LYS SEQRES 6 O 251 LEU THR ILE SER ASP ASP LEU GLY GLN THR THR LEU GLU SEQRES 7 O 251 VAL PHE LYS SER ASP GLY SER THR LEU VAL SER LYS LYS SEQRES 8 O 251 VAL THR SER LYS ASP LYS SER SER GLY GLU GLU LYS PHE SEQRES 9 O 251 ASN GLU LYS GLY GLU VAL SER GLU LYS ILE ILE THR ARG SEQRES 10 O 251 ALA ASP GLY THR ARG LEU GLU TYR THR GLY ILE LYS SER SEQRES 11 O 251 ASP GLY SER GLY LYS ALA LYS GLU VAL LEU LYS GLY TYR SEQRES 12 O 251 VAL LEU GLU GLY THR LEU THR ALA GLU LYS THR THR LEU SEQRES 13 O 251 VAL VAL LYS GLU GLY THR VAL THR LEU SER LYS ASN ILE SEQRES 14 O 251 SER LYS SER GLY ALA VAL SER VAL GLU LEU ASN ASP THR SEQRES 15 O 251 ASP SER SER ALA ALA THR LYS LYS THR ALA ALA TRP ASN SEQRES 16 O 251 SER GLY THR SER THR LEU THR ILE THR VAL ASN SER LYS SEQRES 17 O 251 LYS THR LYS ASP LEU VAL PHE THR SER SER ASN THR ILE SEQRES 18 O 251 THR VAL GLN GLN TYR ASP SER ASN GLY THR SER LEU GLU SEQRES 19 O 251 GLY SER ALA VAL GLU ILE THR LYS LEU ASP GLU ILE LYS SEQRES 20 O 251 ASN ALA LEU LYS HET PG4 O 301 30 HET PG4 O 302 30 HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 2 PG4 2(C8 H18 O5) FORMUL 4 HOH *344(H2 O) HELIX 1 AA1 LYS O 264 LEU O 272 1 9 SHEET 1 AA1 4 VAL O 30 LEU O 34 0 SHEET 2 AA1 4 MET O 38 VAL O 42 -1 O VAL O 42 N VAL O 30 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 THR O 97 PHE O 102 -1 O GLU O 100 N LYS O 87 SHEET 4 AA212 LEU O 109 THR O 115 -1 O VAL O 110 N VAL O 101 SHEET 5 AA212 SER O 121 PHE O 126 -1 O GLU O 124 N LYS O 112 SHEET 6 AA212 VAL O 132 THR O 138 -1 O SER O 133 N LYS O 125 SHEET 7 AA212 ARG O 144 THR O 148 -1 O LEU O 145 N ILE O 137 SHEET 8 AA212 GLY O 156 LEU O 162 -1 O LYS O 159 N GLU O 146 SHEET 9 AA212 TYR O 165 LEU O 171 -1 O LEU O 167 N GLU O 160 SHEET 10 AA212 LYS O 175 GLU O 182 -1 O THR O 177 N THR O 170 SHEET 11 AA212 VAL O 185 SER O 192 -1 O LEU O 187 N VAL O 180 SHEET 12 AA212 VAL O 197 ASP O 203 -1 O SER O 198 N ASN O 190 SHEET 1 AA3 5 LYS O 212 ASN O 217 0 SHEET 2 AA3 5 THR O 222 VAL O 227 -1 O THR O 226 N THR O 213 SHEET 3 AA3 5 LYS O 230 PHE O 237 -1 O THR O 232 N ILE O 225 SHEET 4 AA3 5 ILE O 243 GLN O 247 -1 O GLN O 246 N ASP O 234 SHEET 5 AA3 5 VAL O 260 GLU O 261 -1 O VAL O 260 N VAL O 245 SITE 1 AC1 5 ASP O 59 LEU O 61 LYS O 80 VAL O 101 SITE 2 AC1 5 SER O 111 SITE 1 AC2 3 LYS O 135 ILE O 137 TYR O 147 CRYST1 33.039 54.446 66.070 90.00 100.39 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 0.030267 0.000000 0.005550 0.00000 SCALE2 0.000000 0.018367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015388 0.00000