HEADER SUGAR BINDING PROTEIN 16-AUG-18 6EF7 TITLE GSPB SIGLEC DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLATELET BINDING PROTEIN GSPB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SER-RICH 2 (SSR2) SIGLEC DOMAIN RESIDUES 399-521; COMPND 5 SYNONYM: SERINE-RICH ADHESIN FOR PLATELETS,SERINE-RICH REPEAT PROTEIN COMPND 6 GSPB; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS GORDONII; SOURCE 3 ORGANISM_TAXID: 1302; SOURCE 4 GENE: GSPB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LECTIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.M.IVERSON REVDAT 2 01-JUN-22 6EF7 1 JRNL REVDAT 1 19-FEB-20 6EF7 0 JRNL AUTH B.A.BENSING,H.E.STUBBS,R.AGARWAL,I.YAMAKAWA,K.LUONG, JRNL AUTH 2 K.SOLAKYILDIRIM,H.YU,A.HADADIANPOUR,M.A.CASTRO, JRNL AUTH 3 K.P.FIALKOWSKI,K.M.MORRISON,Z.WAWRZAK,X.CHEN,C.B.LEBRILLA, JRNL AUTH 4 J.BAUDRY,J.C.SMITH,P.M.SULLAM,T.M.IVERSON JRNL TITL ORIGINS OF GLYCAN SELECTIVITY IN STREPTOCOCCAL SIGLEC-LIKE JRNL TITL 2 ADHESINS SUGGEST MECHANISMS OF RECEPTOR ADAPTATION. JRNL REF NAT COMMUN V. 13 2753 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35585145 JRNL DOI 10.1038/S41467-022-30509-Y REMARK 2 REMARK 2 RESOLUTION. 1.03 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 54668 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.126 REMARK 3 R VALUE (WORKING SET) : 0.125 REMARK 3 FREE R VALUE : 0.141 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2767 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 39.0682 - 2.7956 0.99 2893 168 0.1552 0.1726 REMARK 3 2 2.7956 - 2.2190 0.99 2776 143 0.1506 0.1528 REMARK 3 3 2.2190 - 1.9385 0.98 2768 116 0.1231 0.1254 REMARK 3 4 1.9385 - 1.7613 0.98 2700 139 0.1276 0.1359 REMARK 3 5 1.7613 - 1.6350 0.97 2670 131 0.1185 0.1391 REMARK 3 6 1.6350 - 1.5386 0.97 2688 120 0.1076 0.1174 REMARK 3 7 1.5386 - 1.4616 0.96 2628 136 0.1043 0.1218 REMARK 3 8 1.4616 - 1.3980 0.96 2607 152 0.1022 0.1105 REMARK 3 9 1.3980 - 1.3441 0.96 2592 139 0.1043 0.1352 REMARK 3 10 1.3441 - 1.2977 0.95 2557 160 0.1069 0.1255 REMARK 3 11 1.2977 - 1.2572 0.96 2578 138 0.1077 0.1285 REMARK 3 12 1.2572 - 1.2212 0.94 2555 112 0.1004 0.1292 REMARK 3 13 1.2212 - 1.1891 0.94 2514 157 0.0984 0.1341 REMARK 3 14 1.1891 - 1.1601 0.94 2516 134 0.0995 0.1104 REMARK 3 15 1.1601 - 1.1337 0.93 2527 133 0.0974 0.1341 REMARK 3 16 1.1337 - 1.1096 0.93 2494 152 0.1023 0.1207 REMARK 3 17 1.1096 - 1.0874 0.92 2465 143 0.1113 0.1331 REMARK 3 18 1.0874 - 1.0668 0.92 2474 136 0.1203 0.1656 REMARK 3 19 1.0668 - 1.0478 0.91 2462 141 0.1316 0.1472 REMARK 3 20 1.0478 - 1.0300 0.90 2437 117 0.1526 0.1785 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) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.180 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 : 0.008 1061 REMARK 3 ANGLE : 1.010 1465 REMARK 3 CHIRALITY : 0.083 170 REMARK 3 PLANARITY : 0.008 197 REMARK 3 DIHEDRAL : 14.685 379 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 6EF7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000236221. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54763 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.030 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 (%) : 95.4 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.06 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 25% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 16.96000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.48500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.10500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.48500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.96000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.10500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 395 REMARK 465 PRO A 396 REMARK 465 GLY A 397 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 466 CD CE NZ REMARK 470 ARG A 521 CD NE CZ NH1 NH2 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 A 946 DISTANCE = 6.73 ANGSTROMS 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 CA A 601 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 399 OD1 REMARK 620 2 ASP A 399 OD2 52.8 REMARK 620 3 GLU A 401 O 85.0 129.7 REMARK 620 4 ASP A 427 OD1 166.4 133.9 93.8 REMARK 620 5 ASP A 427 OD2 125.7 82.8 147.0 53.5 REMARK 620 6 ASN A 428 OD1 81.9 103.4 94.7 84.7 79.8 REMARK 620 7 ASP A 490 OD2 104.9 80.6 86.7 88.5 95.3 173.1 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 601 DBREF 6EF7 A 399 521 UNP Q939N5 GSPB_STRGN 399 521 SEQADV 6EF7 GLY A 395 UNP Q939N5 EXPRESSION TAG SEQADV 6EF7 PRO A 396 UNP Q939N5 EXPRESSION TAG SEQADV 6EF7 GLY A 397 UNP Q939N5 EXPRESSION TAG SEQADV 6EF7 SER A 398 UNP Q939N5 EXPRESSION TAG SEQADV 6EF7 SER A 444 UNP Q939N5 ASN 444 CONFLICT SEQRES 1 A 127 GLY PRO GLY SER ASP THR GLU ARG PRO VAL VAL ASN VAL SEQRES 2 A 127 PRO SER GLU ILE THR VAL TYR ARG GLY GLU SER PHE GLU SEQRES 3 A 127 TYR PHE ALA THR VAL THR ASP ASN SER ASN ALA PHE ASP SEQRES 4 A 127 LEU ALA LYS THR VAL VAL ARG TRP LEU TYR SER ASN GLN SEQRES 5 A 127 PRO GLY ARG GLY THR GLU TRP LEU GLN TYR SER VAL THR SEQRES 6 A 127 GLN VAL GLY ASN GLN LEU LYS VAL ARG ILE PHE GLY ASN SEQRES 7 A 127 VAL PRO ILE ASP THR THR ILE GLY ASP TYR THR ARG TYR SEQRES 8 A 127 VAL VAL ALA THR ASP ALA ALA GLY ASN VAL ASN ALA THR SEQRES 9 A 127 GLN THR GLU MET GLY ASN ALA ALA VAL ASP LYS THR SER SEQRES 10 A 127 VAL ASN GLY GLN PHE LYS LEU ILE ILE ARG HET CA A 601 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *246(H2 O) HELIX 1 AA1 ASP A 433 THR A 437 5 5 HELIX 2 AA2 THR A 498 LYS A 509 1 12 SHEET 1 AA1 4 VAL A 404 ASN A 406 0 SHEET 2 AA1 4 SER A 418 THR A 426 -1 O THR A 424 N ASN A 406 SHEET 3 AA1 4 GLN A 464 ASN A 472 -1 O VAL A 467 N ALA A 423 SHEET 4 AA1 4 GLN A 455 VAL A 461 -1 N THR A 459 O LYS A 466 SHEET 1 AA2 4 GLU A 410 TYR A 414 0 SHEET 2 AA2 4 GLN A 515 ARG A 521 1 O ILE A 519 N ILE A 411 SHEET 3 AA2 4 GLY A 480 VAL A 487 -1 N GLY A 480 O ILE A 520 SHEET 4 AA2 4 VAL A 438 ARG A 440 -1 N VAL A 438 O VAL A 487 LINK OD1 ASP A 399 CA CA A 601 1555 1555 2.49 LINK OD2 ASP A 399 CA CA A 601 1555 1555 2.43 LINK O GLU A 401 CA CA A 601 1555 1555 2.30 LINK OD1 ASP A 427 CA CA A 601 1555 1555 2.45 LINK OD2 ASP A 427 CA CA A 601 1555 1555 2.45 LINK OD1 ASN A 428 CA CA A 601 1555 1555 2.38 LINK OD2 ASP A 490 CA CA A 601 1555 1555 2.32 SITE 1 AC1 5 ASP A 399 GLU A 401 ASP A 427 ASN A 428 SITE 2 AC1 5 ASP A 490 CRYST1 33.920 46.210 72.970 90.00 90.00 90.00 P 21 21 21 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 0.029481 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021640 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013704 0.00000