HEADER SUGAR BINDING PROTEIN 03-DEC-12 4I8E OBSLTE 13-APR-16 4I8E 5IUC TITLE GSPB PLUS ALPHA-2,3-SIALYL (1-THIOETHYL)GALACTOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLATELET BINDING PROTEIN GSPB; COMPND 3 CHAIN: X; COMPND 4 FRAGMENT: UNP RESIDUES 233-617; COMPND 5 SYNONYM: SERINE-RICH ADHESIN FOR PLATELETS, SERINE-RICH REPEAT COMPND 6 PROTEIN 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; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-3X KEYWDS CARBOHYDRATE, ANTIGEN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.M.PYBURN,B.A.BENSING,Y.Q.XIONG,B.J.MELANCON,T.M.TOMASIAK,N.J.WARD, AUTHOR 2 V.YANKOVSKAYA,K.M.OLIVER,G.CECCHINI,G.A.SULIKOWSKI,M.J.TYSKA, AUTHOR 3 P.M.SULLAM,T.M.IVERSON REVDAT 2 13-APR-16 4I8E 1 OBSLTE REVDAT 1 26-DEC-12 4I8E 0 SPRSDE 26-DEC-12 4I8E 3QD1 JRNL AUTH T.M.PYBURN,B.A.BENSING,Y.Q.XIONG,B.J.MELANCON,T.M.TOMASIAK, JRNL AUTH 2 N.J.WARD,V.YANKOVSKAYA,K.M.OLIVER,G.CECCHINI,G.A.SULIKOWSKI, JRNL AUTH 3 M.J.TYSKA,P.M.SULLAM,T.M.IVERSON JRNL TITL A STRUCTURAL MODEL FOR BINDING OF THE SERINE-RICH REPEAT JRNL TITL 2 ADHESIN GSPB TO HOST CARBOHYDRATE RECEPTORS. JRNL REF PLOS PATHOG. V. 7 02112 2011 JRNL REFN ISSN 1553-7366 JRNL PMID 21765814 JRNL DOI 10.1371/JOURNAL.PPAT.1002112 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 29881 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1477 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1987 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2775 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.150 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.136 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.993 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2879 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3937 ; 1.301 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 367 ; 6.242 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;37.447 ;24.851 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 474 ;13.746 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;18.793 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 474 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2165 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1779 ; 0.635 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2914 ; 1.195 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1100 ; 2.058 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1016 ; 3.458 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : X 245 X 398 REMARK 3 ORIGIN FOR THE GROUP (A): 5.4058 2.5290 37.9554 REMARK 3 T TENSOR REMARK 3 T11: 0.0845 T22: 0.0484 REMARK 3 T33: 0.0419 T12: 0.0253 REMARK 3 T13: -0.0068 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.6912 L22: 0.3317 REMARK 3 L33: 2.6958 L12: 0.3098 REMARK 3 L13: -1.0429 L23: -0.6225 REMARK 3 S TENSOR REMARK 3 S11: 0.0158 S12: -0.0460 S13: 0.0041 REMARK 3 S21: -0.0832 S22: -0.0528 S23: -0.0165 REMARK 3 S31: 0.2126 S32: 0.2159 S33: 0.0369 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : X 399 X 523 REMARK 3 ORIGIN FOR THE GROUP (A): -23.3584 -2.4550 79.8577 REMARK 3 T TENSOR REMARK 3 T11: 0.0220 T22: 0.0613 REMARK 3 T33: 0.0834 T12: -0.0026 REMARK 3 T13: -0.0168 T23: -0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.5127 L22: 0.3835 REMARK 3 L33: 0.8193 L12: 0.1746 REMARK 3 L13: -0.2690 L23: -0.2590 REMARK 3 S TENSOR REMARK 3 S11: -0.0118 S12: -0.0891 S13: -0.0059 REMARK 3 S21: -0.0224 S22: 0.0108 S23: 0.0683 REMARK 3 S31: 0.0308 S32: -0.0630 S33: 0.0010 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : X 524 X 603 REMARK 3 ORIGIN FOR THE GROUP (A): -45.4515 3.8012 106.7697 REMARK 3 T TENSOR REMARK 3 T11: 0.0214 T22: 0.3063 REMARK 3 T33: 0.1301 T12: 0.0551 REMARK 3 T13: 0.0226 T23: -0.0434 REMARK 3 L TENSOR REMARK 3 L11: 3.1730 L22: 0.9095 REMARK 3 L33: 0.9481 L12: -1.3962 REMARK 3 L13: -0.8284 L23: 0.5986 REMARK 3 S TENSOR REMARK 3 S11: -0.1167 S12: -0.3955 S13: 0.2227 REMARK 3 S21: 0.0895 S22: 0.0850 S23: 0.0700 REMARK 3 S31: 0.0370 S32: -0.1131 S33: 0.0317 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 4I8E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-12. REMARK 100 THE RCSB ID CODE IS RCSB076433. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-10 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.4 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-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07806 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 : 29986 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: MOLECULAR REPLACEMENT 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 (%): 46.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6 MG/ML GSPB IN BUFFER CONTAINING 1 MM REMARK 280 ALPHA-2,3-SIALYL(1-THIOETHYL)GALACTOSE AND 20 MM TRIS, 8% REMARK 280 PEG3350, 7.5MM COCL2, 7.5MM NICL2, 7.5MM CDCL2, 7.5MM MGCL2, 0.1M REMARK 280 HEPES, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296.15K 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 17.01450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 X 230 REMARK 465 ILE X 231 REMARK 465 PRO X 232 REMARK 465 GLU X 233 REMARK 465 ALA X 234 REMARK 465 SER X 235 REMARK 465 SER X 236 REMARK 465 GLN X 237 REMARK 465 THR X 238 REMARK 465 GLY X 239 REMARK 465 ARG X 240 REMARK 465 ARG X 241 REMARK 465 ARG X 242 REMARK 465 THR X 243 REMARK 465 ARG X 244 REMARK 465 SER X 604 REMARK 465 ILE X 605 REMARK 465 SER X 606 REMARK 465 LYS X 607 REMARK 465 SER X 608 REMARK 465 GLN X 609 REMARK 465 SER X 610 REMARK 465 THR X 611 REMARK 465 SER X 612 REMARK 465 ASN X 613 REMARK 465 SER X 614 REMARK 465 ILE X 615 REMARK 465 SER X 616 REMARK 465 VAL X 617 REMARK 465 ASN X 618 REMARK 465 SER X 619 REMARK 465 SER X 620 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 HIS X 257 115.88 -165.98 REMARK 500 ASP X 262 20.61 -146.13 REMARK 500 LYS X 290 -142.52 57.81 REMARK 500 ASN X 322 140.37 169.45 REMARK 500 SER X 323 88.11 153.03 REMARK 500 ALA X 326 -54.14 93.50 REMARK 500 THR X 381 -94.65 -117.58 REMARK 500 ASN X 430 18.72 57.51 REMARK 500 PHE X 597 1.47 -150.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 IN THE ORIGINAL COORDINATES (3QD1), THE OCCUPANCY OF THE REMARK 600 DISACCHARIDE WAS SET TO 0.15. WHILE THIS ELECTRON DENSITY ONLY REMARK 600 APPEARED IN THIS LOCATION WHEN GSPB WAS CRYSTALLIZED IN THE REMARK 600 PRESENCE OF THIS GLYCAN, THE PDB HAS BEEN MODIFIED (4I8E) WITH THE REMARK 600 OCCUPANCY SET TO 0.0 SINCE WE WERE UNABLE TO MODEL THE GLYCAN TO REMARK 600 PERFECTLY FIT THE DENSITY. THE PRECISE LOCATION WAS NOT PINPOINTED REMARK 600 AND CLOSE CONTACTS WERE OBSERVED. HOWEVER, THIS LOCATION WAS PROVEN REMARK 600 FUNCTIONALLY IMPORTANT THROUGH MULTIPLE IN VITRO AND IN VIVO REMARK 600 EXPERIMENTS. WE THEREFORE BELIEVE THAT IT IS IMPORTANT TO INDICATE REMARK 600 THE LOCATION OF THE DISACCHARIDE AND ITS INTERACTIONS WITH GSPB. REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 RMY X 704 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 NI X 705 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS X 257 NE2 REMARK 620 2 HOH X 839 O 92.7 REMARK 620 3 HOH X 805 O 85.4 167.3 REMARK 620 4 HOH X 827 O 96.2 84.7 83.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD X 702 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU X 401 O REMARK 620 2 ASP X 427 OD2 93.1 REMARK 620 3 ASP X 399 OD2 128.2 134.7 REMARK 620 4 ASN X 428 OD1 93.5 83.1 108.4 REMARK 620 5 ASP X 490 OD2 83.0 91.4 78.1 173.4 REMARK 620 6 ASP X 427 OD1 146.4 53.6 84.8 79.4 100.4 REMARK 620 7 ASP X 399 OD1 83.3 166.6 54.4 84.2 100.9 127.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG X 707 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH X 811 O REMARK 620 2 HOH X 809 O 124.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA X 706 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN X 463 O REMARK 620 2 ASP X 427 O 129.6 REMARK 620 3 ASN X 430 OD1 92.9 63.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL X 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD X 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL X 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RMY X 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI X 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA X 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 707 DBREF 4I8E X 233 617 UNP Q939N5 GSPB_STRGN 233 617 SEQADV 4I8E SER X 444 UNP Q939N5 ASN 444 ENGINEERED MUTATION SEQRES 1 X 391 GLY ILE PRO GLU ALA SER SER GLN THR GLY ARG ARG ARG SEQRES 2 X 391 THR ARG ARG ALA VAL THR GLU SER ALA PRO ASN VAL GLU SEQRES 3 X 391 TYR HIS ASP VAL LYS GLY ASP MET ILE GLN SER VAL THR SEQRES 4 X 391 THR SER PHE ASP ASP THR SER ARG LEU LEU THR TRP THR SEQRES 5 X 391 ILE ASN LEU THR PRO ARG GLN VAL LYS SER ASN LEU GLY SEQRES 6 X 391 ALA LEU VAL SER ILE SER GLY ASN GLN GLU THR ARG THR SEQRES 7 X 391 VAL THR ILE ASN GLY LYS ASN ALA ALA ASN GLY GLY VAL SEQRES 8 X 391 TYR ASN SER GLY GLY ALA TRP ASN LEU TYR THR GLY GLU SEQRES 9 X 391 SER VAL ASN ASN ASN VAL LEU ARG ILE THR THR GLN VAL SEQRES 10 X 391 ASN ASP THR GLY GLY GLU VAL LYS LEU GLY LEU ARG LEU SEQRES 11 X 391 VAL THR SER ASP LYS LYS ILE THR LYS THR ASN LEU PRO SEQRES 12 X 391 LEU GLU PHE SER GLN VAL ALA ALA THR THR ASN GLY SER SEQRES 13 X 391 TRP ASP LYS ALA GLY TYR ASN THR THR ILE VAL GLU LYS SEQRES 14 X 391 ASP THR GLU ARG PRO VAL VAL ASN VAL PRO SER GLU ILE SEQRES 15 X 391 THR VAL TYR ARG GLY GLU SER PHE GLU TYR PHE ALA THR SEQRES 16 X 391 VAL THR ASP ASN SER ASN ALA PHE ASP LEU ALA LYS THR SEQRES 17 X 391 VAL VAL ARG TRP LEU TYR SER ASN GLN PRO GLY ARG GLY SEQRES 18 X 391 THR GLU TRP LEU GLN TYR SER VAL THR GLN VAL GLY ASN SEQRES 19 X 391 GLN LEU LYS VAL ARG ILE PHE GLY ASN VAL PRO ILE ASP SEQRES 20 X 391 THR THR ILE GLY ASP TYR THR ARG TYR VAL VAL ALA THR SEQRES 21 X 391 ASP ALA ALA GLY ASN VAL ASN ALA THR GLN THR GLU MET SEQRES 22 X 391 GLY ASN ALA ALA VAL ASP LYS THR SER VAL ASN GLY GLN SEQRES 23 X 391 PHE LYS LEU ILE ILE ARG PHE ARG ILE LYS THR PRO GLU SEQRES 24 X 391 ASN THR VAL PHE VAL ASN ASN PRO ASN GLN LEU THR GLU SEQRES 25 X 391 VAL GLU LYS ASN LEU VAL ARG GLU ALA VAL LYS LYS SER SEQRES 26 X 391 ASN PRO ASP LEU ARG ALA GLN ASP VAL LEU ASN SER ASN SEQRES 27 X 391 TYR VAL THR GLY ILE THR VAL SER ASN ASN GLY THR THR SEQRES 28 X 391 THR ILE THR TYR ARG ASP GLY ARG LYS ASP ILE ILE ASP SEQRES 29 X 391 GLY SER LYS PHE ILE ASP THR ARG ALA GLY SER ILE SER SEQRES 30 X 391 LYS SER GLN SER THR SER ASN SER ILE SER VAL ASN SER SEQRES 31 X 391 SER HET GOL X 701 6 HET CD X 702 1 HET GOL X 703 6 HET RMY X 704 34 HET NI X 705 1 HET NA X 706 1 HET MG X 707 1 HETNAM GOL GLYCEROL HETNAM CD CADMIUM ION HETNAM RMY ETHYL 3-O-[5-(ACETYLAMINO)-3,5-DIDEOXY-D-GLYCERO-ALPHA- HETNAM 2 RMY D-GALACTO-NON-2-ULOPYRANONOSYL]-1-THIO-BETA-D- HETNAM 3 RMY GALACTOPYRANOSIDE HETNAM NI NICKEL (II) ION HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN RMY ALPHA-2,3-SIALYL (1-THIOETHYL)GALACTOSE FORMUL 2 GOL 2(C3 H8 O3) FORMUL 3 CD CD 2+ FORMUL 5 RMY C19 H33 N O13 S FORMUL 6 NI NI 2+ FORMUL 7 NA NA 1+ FORMUL 8 MG MG 2+ FORMUL 9 HOH *213(H2 O) HELIX 1 1 GLU X 374 VAL X 378 5 5 HELIX 2 2 ASP X 433 THR X 437 5 5 HELIX 3 3 THR X 498 LYS X 509 1 12 HELIX 4 4 THR X 540 ASN X 555 1 16 HELIX 5 5 ARG X 559 SER X 566 5 8 HELIX 6 6 ASN X 567 GLY X 571 1 5 HELIX 7 7 ASP X 593 LYS X 596 5 4 SHEET 1 A 6 VAL X 247 SER X 250 0 SHEET 2 A 6 ILE X 264 ASP X 272 -1 O THR X 269 N SER X 250 SHEET 3 A 6 LEU X 277 LEU X 284 -1 O ASN X 283 N GLN X 265 SHEET 4 A 6 ASN X 338 VAL X 346 -1 O LEU X 340 N ILE X 282 SHEET 5 A 6 GLN X 303 ILE X 310 -1 N ARG X 306 O THR X 343 SHEET 6 A 6 LYS X 313 ASN X 314 -1 O LYS X 313 N ILE X 310 SHEET 1 B 6 ASN X 253 HIS X 257 0 SHEET 2 B 6 TRP X 386 ILE X 395 -1 O GLY X 390 N TYR X 256 SHEET 3 B 6 GLY X 351 SER X 362 -1 N VAL X 353 O THR X 393 SHEET 4 B 6 ASN X 292 ILE X 299 -1 N ASN X 292 O SER X 362 SHEET 5 B 6 TRP X 327 GLU X 333 -1 O TYR X 330 N ALA X 295 SHEET 6 B 6 ALA X 316 VAL X 320 -1 N GLY X 318 O LEU X 329 SHEET 1 C 4 VAL X 404 ASN X 406 0 SHEET 2 C 4 SER X 418 THR X 426 -1 O THR X 424 N ASN X 406 SHEET 3 C 4 GLN X 464 ASN X 472 -1 O ILE X 469 N TYR X 421 SHEET 4 C 4 GLN X 455 VAL X 461 -1 N THR X 459 O LYS X 466 SHEET 1 D 4 GLU X 410 TYR X 414 0 SHEET 2 D 4 GLN X 515 ARG X 521 1 O ILE X 519 N VAL X 413 SHEET 3 D 4 GLY X 480 VAL X 487 -1 N TYR X 482 O LEU X 518 SHEET 4 D 4 VAL X 438 ARG X 440 -1 N ARG X 440 O TYR X 485 SHEET 1 E 2 VAL X 531 VAL X 533 0 SHEET 2 E 2 ILE X 598 THR X 600 1 O ASP X 599 N VAL X 531 SHEET 1 F 3 ILE X 572 VAL X 574 0 SHEET 2 F 3 THR X 580 THR X 583 -1 O THR X 581 N THR X 573 SHEET 3 F 3 LYS X 589 ILE X 592 -1 O ILE X 592 N THR X 580 LINK NE2 HIS X 257 NI NI X 705 1555 1555 2.09 LINK NI NI X 705 O HOH X 839 1555 1555 2.09 LINK NI NI X 705 O HOH X 805 1555 1555 2.18 LINK NI NI X 705 O HOH X 827 1555 1555 2.21 LINK O GLU X 401 CD CD X 702 1555 1555 2.32 LINK OD2 ASP X 427 CD CD X 702 1555 1555 2.33 LINK OD2 ASP X 399 CD CD X 702 1555 1555 2.36 LINK OD1 ASN X 428 CD CD X 702 1555 1555 2.37 LINK OD2 ASP X 490 CD CD X 702 1555 1555 2.43 LINK OD1 ASP X 427 CD CD X 702 1555 1555 2.46 LINK OD1 ASP X 399 CD CD X 702 1555 1555 2.50 LINK MG MG X 707 O HOH X 811 1555 1555 2.70 LINK O ASN X 463 NA NA X 706 1555 1555 2.76 LINK MG MG X 707 O HOH X 809 1555 1555 2.76 LINK O ASP X 427 NA NA X 706 1555 1555 3.00 LINK OD1 ASN X 430 NA NA X 706 1555 1555 3.03 CISPEP 1 ASN X 322 SER X 323 0 -8.57 CISPEP 2 SER X 323 GLY X 324 0 -29.05 SITE 1 AC1 7 ASP X 262 MET X 263 ILE X 264 THR X 285 SITE 2 AC1 7 HOH X 944 HOH X 945 HOH X 966 SITE 1 AC2 5 ASP X 399 GLU X 401 ASP X 427 ASN X 428 SITE 2 AC2 5 ASP X 490 SITE 1 AC3 6 ALA X 505 LYS X 509 THR X 510 SER X 511 SITE 2 AC3 6 GLN X 515 HOH X 938 SITE 1 AC4 15 TRP X 441 LEU X 442 TYR X 443 ARG X 449 SITE 2 AC4 15 ASP X 481 TYR X 482 THR X 483 ARG X 484 SITE 3 AC4 15 ALA X 506 VAL X 507 HOH X 997 HOH X 999 SITE 4 AC4 15 HOH X1001 HOH X1002 HOH X1013 SITE 1 AC5 4 HIS X 257 HOH X 805 HOH X 827 HOH X 839 SITE 1 AC6 4 THR X 426 ASP X 427 ASN X 430 ASN X 463 SITE 1 AC7 5 VAL X 405 ASN X 406 VAL X 407 HOH X 809 SITE 2 AC7 5 HOH X 811 CRYST1 69.900 34.029 83.394 90.00 99.16 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 0.014306 0.000000 0.002306 0.00000 SCALE2 0.000000 0.029387 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012146 0.00000