HEADER IMMUNE SYSTEM 01-SEP-22 8EC3 TITLE THE CRYSTAL STRUCTURE OF THE COMPLEMENT INHIBITORY DOMAIN OF BORRELIA TITLE 2 HERMSII FBPC. COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBRONECTIN-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORRELIA HERMSII HS1; SOURCE 3 ORGANISM_TAXID: 1867252; SOURCE 4 GENE: CIHC, A0V01_04335, BHA007; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PT7HMT KEYWDS BORRELIA HERMSII, COMPLEMENT, INHIBITOR, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR C.E.BOOTH,B.L.GARCIA REVDAT 3 03-APR-24 8EC3 1 REMARK REVDAT 2 17-JAN-24 8EC3 1 JRNL REVDAT 1 07-JUN-23 8EC3 0 JRNL AUTH S.ROY,C.E.BOOTH JR.,A.D.POWELL-PIERCE,A.M.SCHULZ,J.T.SKARE, JRNL AUTH 2 B.L.GARCIA JRNL TITL CONFORMATIONAL DYNAMICS OF COMPLEMENT PROTEASE C1R INHIBITOR JRNL TITL 2 PROTEINS FROM LYME DISEASE- AND RELAPSING FEVER-CAUSING JRNL TITL 3 SPIROCHETES. JRNL REF J.BIOL.CHEM. V. 299 04972 2023 JRNL REFN ESSN 1083-351X JRNL PMID 37380082 JRNL DOI 10.1016/J.JBC.2023.104972 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.ROY,C.E.BOOTH,A.D.POWELL-PIERCE,A.M.SCHULZ,J.T.SKARE, REMARK 1 AUTH 2 B.L.GARCIA REMARK 1 TITL "CONFORMATIONAL DYNAMICS OF C1R INHIBITOR PROTEINS FROM LYME REMARK 1 TITL 2 DISEASE AND RELAPSING FEVER SPIROCHETES". REMARK 1 REF BIORXIV 2023 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 36909632 REMARK 1 DOI 10.1101/2023.03.01.530473 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 22688 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.460 REMARK 3 FREE R VALUE TEST SET COUNT : 1919 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 31.2800 - 3.6200 0.99 1593 150 0.1759 0.1944 REMARK 3 2 3.6100 - 2.8700 1.00 1581 143 0.1637 0.1736 REMARK 3 3 2.8700 - 2.5100 1.00 1558 141 0.1738 0.1846 REMARK 3 4 2.5100 - 2.2800 1.00 1564 153 0.1634 0.1708 REMARK 3 5 2.2800 - 2.1200 1.00 1560 136 0.1650 0.2135 REMARK 3 6 2.1100 - 1.9900 1.00 1541 151 0.1768 0.2169 REMARK 3 7 1.9900 - 1.8900 0.98 1537 136 0.1871 0.2313 REMARK 3 8 1.8900 - 1.8100 0.97 1500 146 0.1924 0.2513 REMARK 3 9 1.8100 - 1.7400 0.97 1509 148 0.1997 0.2671 REMARK 3 10 1.7400 - 1.6800 0.95 1478 126 0.1959 0.2582 REMARK 3 11 1.6800 - 1.6300 0.94 1472 123 0.2146 0.2345 REMARK 3 12 1.6300 - 1.5800 0.91 1418 143 0.2233 0.2378 REMARK 3 13 1.5800 - 1.5400 0.85 1310 117 0.2463 0.2808 REMARK 3 14 1.5400 - 1.5000 0.74 1148 106 0.2627 0.2665 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) : 0.159 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.946 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.39 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 : 0.010 1247 REMARK 3 ANGLE : 1.053 1667 REMARK 3 CHIRALITY : 0.053 189 REMARK 3 PLANARITY : 0.008 212 REMARK 3 DIHEDRAL : 15.723 485 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 8EC3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1000267794. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM 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 : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23546 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 31.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: ALPHAFOLD REMARK 200 REMARK 200 REMARK: LARGE BIREFRINGENT PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN IN THE FOLLOWING REMARK 280 CONDITION CONTAINING 0.2M MAGNESIUM (II) CHLORIDE, 0.1M BIS-TRIS REMARK 280 (PH 5.5), AND 25% PEG 3,350. CRYSTALS WERE CRYOPROTECTED IN A REMARK 280 BUFFER CONTAINING 0.2M MAGNESIUM (II) CHLORIDE, 0.1M SODIUM REMARK 280 CITRATE (PH 5.4), 25% PEG 3,350, AND 10% GLYCEROL., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298.15K 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 23.27850 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: 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 GLY A 207 REMARK 465 MET A 247 REMARK 465 ARG A 248 REMARK 465 MET A 249 REMARK 465 SER A 250 REMARK 465 GLY A 251 REMARK 465 HIS A 252 REMARK 465 SER A 253 REMARK 465 THR A 254 REMARK 465 LYS A 301 REMARK 465 PHE A 302 REMARK 465 SER A 303 REMARK 465 SER A 304 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 O HOH A 641 O HOH A 655 1.85 REMARK 500 OE1 GLU A 212 O HOH A 501 2.13 REMARK 500 O HOH A 608 O HOH A 612 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 A 287 -71.17 -112.98 REMARK 500 REMARK 500 REMARK: NULL 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 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 239 OD1 REMARK 620 2 HOH A 508 O 69.0 REMARK 620 3 HOH A 565 O 77.2 81.2 REMARK 620 4 HOH A 606 O 100.8 95.6 176.7 REMARK 620 N 1 2 3 DBREF 8EC3 A 212 374 UNP G9BXS5 G9BXS5_BORHE 212 374 SEQADV 8EC3 GLY A 207 UNP G9BXS5 EXPRESSION TAG SEQADV 8EC3 SER A 208 UNP G9BXS5 EXPRESSION TAG SEQADV 8EC3 THR A 209 UNP G9BXS5 EXPRESSION TAG SEQADV 8EC3 GLY A 210 UNP G9BXS5 EXPRESSION TAG SEQADV 8EC3 SER A 211 UNP G9BXS5 EXPRESSION TAG SEQRES 1 A 168 GLY SER THR GLY SER GLU TYR TYR ASP GLN LEU LYS LYS SEQRES 2 A 168 ALA GLU LYS ASP ILE ASP SER ALA PHE LYS ILE LEU GLU SEQRES 3 A 168 LYS LEU LYS LYS ASP ARG ASP GLN VAL GLU LEU GLN GLY SEQRES 4 A 168 THR MET ARG MET SER GLY HIS SER THR SER GLU ASP ARG SEQRES 5 A 168 ALA THR ALA GLN ALA LYS LEU ASN GLN PHE SER LYS ALA SEQRES 6 A 168 LYS LEU VAL GLN GLU LEU LYS ASP LEU LEU GLU LYS ILE SEQRES 7 A 168 ASP LYS ASN ALA LYS LEU THR ILE ASP ASN ALA VAL GLU SEQRES 8 A 168 ASP PHE SER LYS PHE SER SER GLU THR PRO GLN SER ASN SEQRES 9 A 168 TYR VAL THR GLU ALA ASP LYS SER LEU TYR LEU ALA LYS SEQRES 10 A 168 ASP LYS LEU TYR ASP LEU ILE LYS ALA VAL GLU SER SER SEQRES 11 A 168 ALA ASN THR TYR ASP ALA TYR ALA LYS ARG THR GLY ILE SEQRES 12 A 168 GLY HIS GLY SER LYS PHE SER GLU VAL GLU ASN HIS LEU SEQRES 13 A 168 LYS ASP ALA LYS SER LEU ILE LYS LYS ALA LEU LYS HET MG A 401 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *157(H2 O) HELIX 1 AA1 GLY A 210 GLY A 245 1 36 HELIX 2 AA2 ARG A 258 ASN A 266 1 9 HELIX 3 AA3 SER A 269 ASN A 287 1 19 HELIX 4 AA4 ASN A 287 SER A 300 1 14 HELIX 5 AA5 THR A 306 SER A 335 1 30 HELIX 6 AA6 ASN A 338 LYS A 345 1 8 HELIX 7 AA7 LYS A 354 LEU A 373 1 20 LINK OD1 ASP A 239 MG MG A 401 1555 1555 2.38 LINK MG MG A 401 O HOH A 508 1555 1555 1.99 LINK MG MG A 401 O HOH A 565 1555 1555 2.60 LINK MG MG A 401 O HOH A 606 1555 1655 2.64 CRYST1 38.239 46.557 45.186 90.00 110.80 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 0.026151 0.000000 0.009933 0.00000 SCALE2 0.000000 0.021479 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023673 0.00000