HEADER VIRAL PROTEIN 13-MAR-18 5ZHG 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-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 5 PPPARG4; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1182032 KEYWDS GROUP C ROTAVIRUS, VP8*, GALACTIN-LIKE, HISTO-BLOOD GROUP ANTIGEN., KEYWDS 2 VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.SUN,Z.DUAN REVDAT 3 27-MAR-24 5ZHG 1 REMARK REVDAT 2 06-JUN-18 5ZHG 1 JRNL REVDAT 1 11-APR-18 5ZHG 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. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 18222 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 930 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 38.1376 - 3.4402 1.00 2624 154 0.1701 0.1990 REMARK 3 2 3.4402 - 2.7308 1.00 2523 129 0.1692 0.1929 REMARK 3 3 2.7308 - 2.3857 1.00 2459 139 0.1799 0.2159 REMARK 3 4 2.3857 - 2.1676 1.00 2472 141 0.1611 0.1913 REMARK 3 5 2.1676 - 2.0122 1.00 2455 98 0.1669 0.1513 REMARK 3 6 2.0122 - 1.8936 0.99 2404 147 0.1960 0.2127 REMARK 3 7 1.8936 - 1.7988 0.96 2355 122 0.3567 0.3767 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.62 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 : 0.004 1374 REMARK 3 ANGLE : 0.697 1877 REMARK 3 CHIRALITY : 0.055 199 REMARK 3 PLANARITY : 0.004 241 REMARK 3 DIHEDRAL : 16.621 482 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 39.6356 55.8409 139.6974 REMARK 3 T TENSOR REMARK 3 T11: 0.1256 T22: 0.1232 REMARK 3 T33: 0.1326 T12: 0.0063 REMARK 3 T13: -0.0006 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.4528 L22: 0.4681 REMARK 3 L33: 0.8616 L12: -0.1053 REMARK 3 L13: -0.0914 L23: 0.1890 REMARK 3 S TENSOR REMARK 3 S11: 0.0041 S12: 0.0163 S13: -0.0043 REMARK 3 S21: 0.0336 S22: -0.0021 S23: -0.0015 REMARK 3 S31: 0.0232 S32: 0.0086 S33: -0.0000 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 5ZHG 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_1300007090. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-AUG-17 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : XENOCS GENIX 3D CU HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18290 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.799 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0190 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 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: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 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 19.03250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.00700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.03500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.00700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.03250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.03500 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 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 291 O HOH A 388 1.88 REMARK 500 OD1 ASN A 18 O HOH A 201 1.91 REMARK 500 O HOH A 202 O HOH A 203 1.99 REMARK 500 O HOH A 387 O HOH A 388 1.99 REMARK 500 ND2 ASN A 8 O HOH A 202 2.04 REMARK 500 ND2 ASN A 8 O HOH A 203 2.12 REMARK 500 NZ LYS A 55 O HOH A 204 2.13 REMARK 500 O HOH A 323 O HOH A 371 2.15 REMARK 500 O HOH A 269 O HOH A 302 2.16 REMARK 500 O HOH A 233 O HOH A 388 2.18 REMARK 500 O HOH A 345 O HOH A 364 2.19 REMARK 500 O HOH A 393 O HOH A 403 2.19 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 TRP A 102 -164.04 -126.12 REMARK 500 ASN A 129 -74.21 87.53 REMARK 500 ASN A 149 -154.35 -110.17 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 408 DISTANCE = 6.16 ANGSTROMS DBREF 5ZHG A 1 161 UNP Q82040 VP4_ROTHC 64 224 SEQADV 5ZHG 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 FORMUL 2 HOH *208(H2 O) HELIX 1 AA1 GLU A 12 LEU A 16 5 5 HELIX 2 AA2 VAL A 63 ILE A 68 5 6 HELIX 3 AA3 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 TYR A 53 N VAL A 32 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 CISPEP 1 GLY A 4 PRO A 5 0 0.69 CRYST1 38.065 40.070 124.014 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 0.026271 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024956 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008064 0.00000