HEADER CHAPERONE 30-APR-23 8SOT TITLE STRUCTURE OF THE PPIASE DOMAIN OF BORRELIAL BB0108 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BASIC MEMBRANE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: 6-RESIDUE AMINO ACID INSERTION AT THE C-TER DUE TO A COMPND 6 CLONING ARTIFACT. N-TER INSERTION OF L1.B31 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORRELIELLA BURGDORFERI B31; SOURCE 3 ORGANISM_TAXID: 224326; SOURCE 4 STRAIN: ATCC 35210 / DSM 4680 / CIP 102532 / B31; SOURCE 5 GENE: BB_0108; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-6-P1 KEYWDS PEPTIDYL PROLYL CIS/TRANS ISOMERASE, PARVULIN FOLD, PRSA, SURA, KEYWDS 2 CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR A.K.SHAKYA,O.HERZBERG REVDAT 2 24-APR-24 8SOT 1 JRNL REVDAT 1 11-OCT-23 8SOT 0 JRNL AUTH S.D.FOOR,K.BRANGULIS,A.K.SHAKYA,V.S.RANA,S.BISTA,C.KITSOU, JRNL AUTH 2 M.RONZETTI,A.B.ALREJA,S.B.LINDEN,A.S.ALTIERI,B.BALJINNYAM, JRNL AUTH 3 I.AKOPJANA,D.C.NELSON,A.SIMEONOV,O.HERZBERG,M.J.CAIMANO, JRNL AUTH 4 U.PAL JRNL TITL A UNIQUE BORRELIAL PROTEIN FACILITATES MICROBIAL IMMUNE JRNL TITL 2 EVASION. JRNL REF MBIO V. 14 13523 2023 JRNL REFN ESSN 2150-7511 JRNL PMID 37830812 JRNL DOI 10.1128/MBIO.02135-23 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 13566 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 (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 660 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 31.4700 - 3.4100 0.94 2569 128 0.2022 0.2198 REMARK 3 2 3.4000 - 2.7000 0.97 2589 141 0.2097 0.2709 REMARK 3 3 2.7000 - 2.3600 0.98 2594 127 0.2031 0.2686 REMARK 3 4 2.3600 - 2.1500 0.99 2615 130 0.1855 0.2544 REMARK 3 5 2.1500 - 1.9900 0.96 2539 134 0.1822 0.2673 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.251 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.368 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.03 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 1792 REMARK 3 ANGLE : 0.800 2405 REMARK 3 CHIRALITY : 0.054 267 REMARK 3 PLANARITY : 0.008 316 REMARK 3 DIHEDRAL : 13.562 653 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 8SOT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1000273991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-23 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 : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13591 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 31.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.670 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: RECTANGULAR PLATE SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% 2 PROPANOL, 0.1M BICINE, 30% REMARK 280 PEG1500, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 288.15K 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 50.98400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.41750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.98400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.41750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ASP B 281 REMARK 465 ALA B 282 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 LYS A 184 CG CD CE NZ REMARK 470 GLN A 234 CG CD OE1 NE2 REMARK 470 ASN A 238 CG OD1 ND2 REMARK 470 LEU A 239 CG CD1 CD2 REMARK 470 LYS A 263 CG CD CE NZ REMARK 470 ARG A 277 CG CD NE CZ NH1 NH2 REMARK 470 PRO A 278 CG CD REMARK 470 HIS A 279 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 280 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 181 CG CD CE NZ REMARK 470 ASP B 182 CG OD1 OD2 REMARK 470 LYS B 183 CG CD CE NZ REMARK 470 LYS B 184 CG CD CE NZ REMARK 470 LYS B 246 CG CD CE NZ REMARK 470 ARG B 277 CG CD NE CZ NH1 NH2 REMARK 470 PRO B 278 CG CD REMARK 470 HIS B 279 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B 280 CG CD NE CZ NH1 NH2 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 NH2 ARG A 172 OD1 ASN B 223 2.13 REMARK 500 REMARK 500 REMARK: NULL DBREF 8SOT A 168 276 UNP O51135 O51135_BORBU 168 276 DBREF 8SOT B 168 276 UNP O51135 O51135_BORBU 168 276 SEQADV 8SOT LEU A 167 UNP O51135 EXPRESSION TAG SEQADV 8SOT ARG A 277 UNP O51135 EXPRESSION TAG SEQADV 8SOT PRO A 278 UNP O51135 EXPRESSION TAG SEQADV 8SOT HIS A 279 UNP O51135 EXPRESSION TAG SEQADV 8SOT ARG A 280 UNP O51135 EXPRESSION TAG SEQADV 8SOT ASP A 281 UNP O51135 EXPRESSION TAG SEQADV 8SOT ALA A 282 UNP O51135 EXPRESSION TAG SEQADV 8SOT LEU B 167 UNP O51135 EXPRESSION TAG SEQADV 8SOT ARG B 277 UNP O51135 EXPRESSION TAG SEQADV 8SOT PRO B 278 UNP O51135 EXPRESSION TAG SEQADV 8SOT HIS B 279 UNP O51135 EXPRESSION TAG SEQADV 8SOT ARG B 280 UNP O51135 EXPRESSION TAG SEQADV 8SOT ASP B 281 UNP O51135 EXPRESSION TAG SEQADV 8SOT ALA B 282 UNP O51135 EXPRESSION TAG SEQRES 1 A 116 LEU PRO ASP ILE SER ARG VAL SER HIS ILE PHE PHE SER SEQRES 2 A 116 THR LYS ASP LYS LYS ARG SER ASP VAL LEU ASP GLN ALA SEQRES 3 A 116 LYS ASN ILE LEU SER GLN ILE ARG SER LYS LYS ILE THR SEQRES 4 A 116 PHE GLU GLU ALA VAL ARG LYS TYR SER ASN ASP GLU SER SEQRES 5 A 116 SER LYS ALA LYS ASN GLY ASP LEU GLY PHE LEU SER ARG SEQRES 6 A 116 GLY ASP GLN ASN ALA GLN ASN LEU LEU GLY ALA ASP PHE SEQRES 7 A 116 VAL LYS GLU VAL PHE ASN PHE ASN LYS GLY ASP ILE SER SEQRES 8 A 116 SER PRO ILE ALA SER LYS GLU GLY PHE HIS ILE VAL LYS SEQRES 9 A 116 VAL THR GLU LYS TYR ALA ARG PRO HIS ARG ASP ALA SEQRES 1 B 116 LEU PRO ASP ILE SER ARG VAL SER HIS ILE PHE PHE SER SEQRES 2 B 116 THR LYS ASP LYS LYS ARG SER ASP VAL LEU ASP GLN ALA SEQRES 3 B 116 LYS ASN ILE LEU SER GLN ILE ARG SER LYS LYS ILE THR SEQRES 4 B 116 PHE GLU GLU ALA VAL ARG LYS TYR SER ASN ASP GLU SER SEQRES 5 B 116 SER LYS ALA LYS ASN GLY ASP LEU GLY PHE LEU SER ARG SEQRES 6 B 116 GLY ASP GLN ASN ALA GLN ASN LEU LEU GLY ALA ASP PHE SEQRES 7 B 116 VAL LYS GLU VAL PHE ASN PHE ASN LYS GLY ASP ILE SER SEQRES 8 B 116 SER PRO ILE ALA SER LYS GLU GLY PHE HIS ILE VAL LYS SEQRES 9 B 116 VAL THR GLU LYS TYR ALA ARG PRO HIS ARG ASP ALA HET GOL A 301 6 HET GOL B 301 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *88(H2 O) HELIX 1 AA1 LYS A 184 SER A 201 1 18 HELIX 2 AA2 THR A 205 SER A 214 1 10 HELIX 3 AA3 ASP A 216 ALA A 221 1 6 HELIX 4 AA4 ASP A 233 GLY A 241 1 9 HELIX 5 AA5 GLY A 241 PHE A 249 1 9 HELIX 6 AA6 LYS B 184 SER B 201 1 18 HELIX 7 AA7 THR B 205 SER B 214 1 10 HELIX 8 AA8 ASP B 216 ALA B 221 1 6 HELIX 9 AA9 ASP B 233 GLY B 241 1 9 HELIX 10 AB1 GLY B 241 PHE B 251 1 11 SHEET 1 AA1 4 ASP A 225 SER A 230 0 SHEET 2 AA1 4 ILE A 170 SER A 179 -1 N VAL A 173 O LEU A 226 SHEET 3 AA1 4 GLY A 265 TYR A 275 -1 O PHE A 266 N PHE A 178 SHEET 4 AA1 4 ILE A 260 ALA A 261 -1 N ILE A 260 O HIS A 267 SHEET 1 AA2 4 ASP B 225 SER B 230 0 SHEET 2 AA2 4 ILE B 170 SER B 179 -1 N SER B 171 O LEU B 229 SHEET 3 AA2 4 GLY B 265 TYR B 275 -1 O PHE B 266 N PHE B 178 SHEET 4 AA2 4 ILE B 260 ALA B 261 -1 N ILE B 260 O HIS B 267 CRYST1 101.968 38.835 53.681 90.00 106.00 90.00 C 1 2 1 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 0.009807 0.000000 0.002812 0.00000 SCALE2 0.000000 0.025750 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019379 0.00000