HEADER VIRAL PROTEIN 13-MAR-18 5ZHO TITLE HUMAN GROUP C ROTAVIRUS VP8*S RECOGNIZE TYPE A HISTO-BLOOD GROUP TITLE 2 ANTIGENS AS LIGANDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER CAPSID PROTEIN VP8*; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HEMAGGLUTININ; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN ROTAVIRUS C; SOURCE 3 ORGANISM_TAXID: 31567; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS GROUP C ROTAVIRUS, VP8*, GALACTIN-LIKE, HISTO-BLOOD GROUP ANTIGEN, KEYWDS 2 VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.SUN,Z.DUAN,J.QI REVDAT 4 22-NOV-23 5ZHO 1 HETSYN LINK REVDAT 3 29-JUL-20 5ZHO 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 06-JUN-18 5ZHO 1 JRNL REVDAT 1 11-APR-18 5ZHO 0 JRNL AUTH X.SUN,L.WANG,J.QI,D.LI,M.WANG,X.CONG,R.PENG,W.CHAI,Q.ZHANG, JRNL AUTH 2 H.WANG,H.WEN,G.F.GAO,M.TAN,Z.DUAN JRNL TITL HUMAN GROUP C ROTAVIRUS VP8*S RECOGNIZE TYPE A HISTO-BLOOD JRNL TITL 2 GROUP ANTIGENS AS LIGANDS. JRNL REF J. VIROL. V. 92 2018 JRNL REFN ESSN 1098-5514 JRNL PMID 29593033 JRNL DOI 10.1128/JVI.00442-18 REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 36107 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1739 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 37.8023 - 3.2071 0.99 3071 177 0.1562 0.1759 REMARK 3 2 3.2071 - 2.5457 1.00 2954 150 0.1499 0.1777 REMARK 3 3 2.5457 - 2.2240 0.99 2897 143 0.1384 0.1585 REMARK 3 4 2.2240 - 2.0206 1.00 2895 154 0.1237 0.1480 REMARK 3 5 2.0206 - 1.8758 1.00 2932 109 0.1225 0.1601 REMARK 3 6 1.8758 - 1.7652 0.99 2854 139 0.1221 0.1704 REMARK 3 7 1.7652 - 1.6768 0.99 2863 137 0.1227 0.1758 REMARK 3 8 1.6768 - 1.6038 0.99 2849 148 0.1247 0.1906 REMARK 3 9 1.6038 - 1.5421 0.99 2853 119 0.1308 0.1737 REMARK 3 10 1.5421 - 1.4889 0.98 2781 156 0.1424 0.1973 REMARK 3 11 1.4889 - 1.4423 0.98 2793 156 0.1598 0.2265 REMARK 3 12 1.4423 - 1.4011 0.93 2626 151 0.1909 0.2482 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.18 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 1471 REMARK 3 ANGLE : 0.828 2021 REMARK 3 CHIRALITY : 0.076 224 REMARK 3 PLANARITY : 0.006 259 REMARK 3 DIHEDRAL : 15.495 520 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 5ZHO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300007108. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36324 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.5860 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.56500 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: PHASER REMARK 200 STARTING MODEL: 5ZHG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CHLORIDE, 0.1 M BIS-TRIS REMARK 280 PH 6.5, 1.5 M AMMONIUM SULFATE, EVAPORATION, TEMPERATURE 291K 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 18.99250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.90700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.91050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.90700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.99250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.91050 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 APPLY THE FOLLOWING TO CHAINS: A, 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 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 529 O HOH A 546 2.00 REMARK 500 OD1 ASN A 136 O HOH A 401 2.17 REMARK 500 O HOH A 439 O HOH A 494 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 402 O HOH A 415 3949 2.03 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 129 -16.19 73.20 REMARK 500 ASP A 130 13.36 -148.05 REMARK 500 ASN A 149 -164.84 -101.68 REMARK 500 ASN A 149 -163.98 -101.68 REMARK 500 REMARK 500 REMARK: NULL 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 604 DISTANCE = 6.34 ANGSTROMS DBREF 5ZHO A 1 161 UNP Q82040 VP4_ROTHC 64 224 SEQADV 5ZHO MET A 0 UNP Q82040 INITIATING METHIONINE SEQRES 1 A 162 MET GLU ILE THR GLY PRO HIS THR ASN THR VAL ILE GLU SEQRES 2 A 162 TRP SER ASN LEU ILE ASN THR ASN THR TRP LEU LEU TYR SEQRES 3 A 162 GLN LYS PRO LEU ASN SER VAL ARG LEU LEU LYS HIS GLY SEQRES 4 A 162 PRO ASP THR TYR ASN SER ASN LEU ALA ALA PHE GLU LEU SEQRES 5 A 162 TRP TYR GLY LYS SER GLY THR THR ILE THR SER VAL TYR SEQRES 6 A 162 TYR ASN THR ILE ASN ASN GLN ASN LYS THR HIS ASP ALA SEQRES 7 A 162 ASN SER ASP CYS LEU ILE LEU PHE TRP ASN GLU GLY SER SEQRES 8 A 162 THR GLN LEU GLU LYS GLN VAL VAL THR PHE ASN TRP ASN SEQRES 9 A 162 VAL GLY GLY ILE LEU ILE LYS PRO ILE ASN SER SER ARG SEQRES 10 A 162 MET ARG ILE CYS MET SER GLY MET GLU ASN PHE ASN ASN SEQRES 11 A 162 ASP SER PHE ASN TRP GLU ASN TRP ASN HIS GLU PHE PRO SEQRES 12 A 162 ARG SER ASN PRO GLY ILE ASN ILE ASN MET TYR THR GLU SEQRES 13 A 162 TYR PHE LEU ALA SER SER HET GLA B 1 24 HET FUC B 2 21 HET A2G B 3 25 HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETSYN GLA ALPHA-D-GALACTOSE; D-GALACTOSE; GALACTOSE; ALPHA D- HETSYN 2 GLA GALACTOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN A2G N-ACETYL-ALPHA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 A2G ALPHA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 A2G ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-2-DEOXY-2-AMINO- HETSYN 4 A2G GALACTOSE FORMUL 2 GLA C6 H12 O6 FORMUL 2 FUC C6 H12 O5 FORMUL 2 A2G C8 H15 N O6 FORMUL 3 HOH *204(H2 O) HELIX 1 AA1 GLU A 12 LEU A 16 5 5 HELIX 2 AA2 ASN A 70 ASN A 72 5 3 SHEET 1 AA1 6 GLU A 1 HIS A 6 0 SHEET 2 AA1 6 TYR A 156 SER A 160 -1 O TYR A 156 N HIS A 6 SHEET 3 AA1 6 THR A 21 GLN A 26 -1 N LEU A 24 O PHE A 157 SHEET 4 AA1 6 VAL A 104 ASN A 113 -1 O ILE A 109 N THR A 21 SHEET 5 AA1 6 ARG A 116 PHE A 127 -1 O ARG A 118 N LYS A 110 SHEET 6 AA1 6 SER A 131 PRO A 142 -1 O PHE A 141 N MET A 117 SHEET 1 AA2 6 VAL A 10 ILE A 11 0 SHEET 2 AA2 6 ILE A 150 MET A 152 -1 O ILE A 150 N ILE A 11 SHEET 3 AA2 6 VAL A 32 HIS A 37 -1 N LYS A 36 O ASN A 151 SHEET 4 AA2 6 ALA A 48 GLY A 54 -1 O PHE A 49 N HIS A 37 SHEET 5 AA2 6 CYS A 81 GLU A 88 -1 O CYS A 81 N GLY A 54 SHEET 6 AA2 6 THR A 91 THR A 99 -1 O GLN A 96 N LEU A 84 SHEET 1 AA3 2 THR A 59 THR A 61 0 SHEET 2 AA3 2 THR A 74 ASP A 76 -1 O HIS A 75 N ILE A 60 LINK O2 GLA B 1 C1 FUC B 2 1555 1555 1.44 LINK O3 GLA B 1 C1 A2G B 3 1555 1555 1.44 CISPEP 1 GLY A 4 PRO A 5 0 2.78 CRYST1 37.985 39.821 119.814 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 0.026326 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025112 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008346 0.00000