HEADER VIRAL PROTEIN 23-MAY-17 5VX9 TITLE VP8* OF P[6] HUMAN ROTAVIRUS RV3 IN COMPLEX WITH LNFP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER CAPSID PROTEIN VP4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 65-223; COMPND 5 SYNONYM: ROTAVIRUS RV3 VP8*; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN ROTAVIRUS A; SOURCE 3 ORGANISM_TAXID: 10941; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GLYCAN, HBGA, ROTAVIRUS, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.HU,B.V.VENKATARAM PRASAD REVDAT 4 04-OCT-23 5VX9 1 HETSYN LINK REVDAT 3 29-JUL-20 5VX9 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 11-DEC-19 5VX9 1 REMARK REVDAT 1 18-JUL-18 5VX9 0 JRNL AUTH L.HU,B.SANKARAN,D.R.LAUCIRICA,K.PATIL,W.SALMEN, JRNL AUTH 2 A.C.M.FERREON,P.S.TSOI,Y.LASANAJAK,D.F.SMITH,S.RAMANI, JRNL AUTH 3 R.L.ATMAR,M.K.ESTES,J.C.FERREON,B.V.V.PRASAD JRNL TITL GLYCAN RECOGNITION IN GLOBALLY DOMINANT HUMAN ROTAVIRUSES. JRNL REF NAT COMMUN V. 9 2631 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29980685 JRNL DOI 10.1038/S41467-018-05098-4 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.190 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 13692 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 684 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 34.0890 - 3.7884 0.98 2669 128 0.1336 0.1397 REMARK 3 2 3.7884 - 3.0076 0.98 2659 119 0.1330 0.2013 REMARK 3 3 3.0076 - 2.6276 0.99 2682 138 0.1543 0.1945 REMARK 3 4 2.6276 - 2.3874 0.97 2636 133 0.1523 0.2175 REMARK 3 5 2.3874 - 2.2163 0.98 2650 117 0.1455 0.2112 REMARK 3 6 2.2163 - 2.0857 0.99 2669 139 0.1377 0.2020 REMARK 3 7 2.0857 - 1.9812 0.98 2640 144 0.1459 0.2177 REMARK 3 8 1.9812 - 1.8950 0.98 2613 178 0.1524 0.2845 REMARK 3 9 1.8950 - 1.8220 0.98 2660 130 0.1600 0.2318 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.990 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 : 0.007 1420 REMARK 3 ANGLE : 1.094 1945 REMARK 3 CHIRALITY : 0.052 231 REMARK 3 PLANARITY : 0.004 235 REMARK 3 DIHEDRAL : 13.077 610 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 5VX9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000228099. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.0.9 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13693 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.822 REMARK 200 RESOLUTION RANGE LOW (A) : 31.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 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) : 0.18300 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 2.5.5 REMARK 200 STARTING MODEL: PDB ENTRY 2AEN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, 0.1 M TRIS, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 18.25500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.53500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.31500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.53500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.25500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.31500 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: 1920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL 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: 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 THR A 87 -77.11 -103.27 REMARK 500 THR A 99 -54.95 -125.68 REMARK 500 TYR A 170 -102.72 62.90 REMARK 500 ASN A 192 50.82 -145.12 REMARK 500 REMARK 500 REMARK: NULL DBREF 5VX9 A 65 223 UNP D7F7M7 D7F7M7_9REOV 65 223 SEQADV 5VX9 GLY A 63 UNP D7F7M7 EXPRESSION TAG SEQADV 5VX9 SER A 64 UNP D7F7M7 EXPRESSION TAG SEQRES 1 A 161 GLY SER LEU ASP GLY PRO TYR GLN SER THR SER PHE LYS SEQRES 2 A 161 PRO PRO SER ASP TYR TRP ILE LEU LEU ASN PRO THR ASN SEQRES 3 A 161 GLN GLN VAL VAL LEU GLU GLY THR ASN LYS THR ASP ILE SEQRES 4 A 161 TRP VAL ALA LEU LEU LEU VAL GLU PRO ASN VAL THR ASN SEQRES 5 A 161 GLN SER ARG GLN TYR THR LEU PHE GLY GLU THR LYS GLN SEQRES 6 A 161 ILE THR VAL GLU ASN ASN THR ASN LYS TRP LYS PHE PHE SEQRES 7 A 161 GLU MET PHE ARG SER SER VAL SER ALA GLU PHE GLN HIS SEQRES 8 A 161 LYS ARG THR LEU THR SER ASP THR LYS LEU ALA GLY PHE SEQRES 9 A 161 LEU LYS HIS TYR ASN SER VAL TRP THR PHE HIS GLY GLU SEQRES 10 A 161 THR PRO HIS ALA THR THR ASP TYR SER SER THR SER ASN SEQRES 11 A 161 LEU SER GLU VAL GLU THR THR ILE HIS VAL GLU PHE TYR SEQRES 12 A 161 ILE ILE PRO ARG SER GLN GLU SER LYS CYS VAL GLU TYR SEQRES 13 A 161 ILE ASN THR GLY LEU HET BGC B 1 12 HET GAL B 2 11 HET NAG B 3 14 HET GAL B 4 11 HET FUC B 5 10 HET SO4 A 306 5 HET SO4 A 307 5 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM SO4 SULFATE ION HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 2 BGC C6 H12 O6 FORMUL 2 GAL 2(C6 H12 O6) FORMUL 2 NAG C8 H15 N O6 FORMUL 2 FUC C6 H12 O5 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *194(H2 O) HELIX 1 AA1 ASN A 192 VAL A 196 5 5 HELIX 2 AA2 GLN A 211 GLY A 222 1 12 SHEET 1 AA111 ASP A 66 TYR A 69 0 SHEET 2 AA111 GLU A 203 PRO A 208 -1 O PHE A 204 N TYR A 69 SHEET 3 AA111 TYR A 80 ASN A 85 -1 N TRP A 81 O ILE A 207 SHEET 4 AA111 ALA A 164 HIS A 169 -1 O ALA A 164 N LEU A 84 SHEET 5 AA111 SER A 172 GLU A 179 -1 O TRP A 174 N LEU A 167 SHEET 6 AA111 GLN A 152 SER A 159 1 N THR A 158 O GLY A 178 SHEET 7 AA111 TRP A 137 ARG A 144 -1 N TRP A 137 O SER A 159 SHEET 8 AA111 TRP A 102 VAL A 108 -1 N ALA A 104 O MET A 142 SHEET 9 AA111 VAL A 91 THR A 96 -1 N GLY A 95 O VAL A 103 SHEET 10 AA111 GLU A 197 ILE A 200 -1 O THR A 199 N GLU A 94 SHEET 11 AA111 THR A 72 PHE A 74 -1 N THR A 72 O ILE A 200 SHEET 1 AA2 6 ASP A 66 TYR A 69 0 SHEET 2 AA2 6 GLU A 203 PRO A 208 -1 O PHE A 204 N TYR A 69 SHEET 3 AA2 6 TYR A 80 ASN A 85 -1 N TRP A 81 O ILE A 207 SHEET 4 AA2 6 ALA A 164 HIS A 169 -1 O ALA A 164 N LEU A 84 SHEET 5 AA2 6 SER A 172 GLU A 179 -1 O TRP A 174 N LEU A 167 SHEET 6 AA2 6 THR A 184 SER A 189 -1 O THR A 184 N HIS A 177 SHEET 1 AA3 2 VAL A 112 LEU A 121 0 SHEET 2 AA3 2 GLU A 124 ASN A 132 -1 O LYS A 126 N TYR A 119 LINK O4 BGC B 1 C1 GAL B 2 1555 1555 1.42 LINK O3 GAL B 2 C1 NAG B 3 1555 1555 1.41 LINK O3 NAG B 3 C1 GAL B 4 1555 1555 1.43 LINK O2 GAL B 4 C1 FUC B 5 1555 1555 1.44 CISPEP 1 GLY A 67 PRO A 68 0 6.27 CISPEP 2 THR A 180 PRO A 181 0 3.52 CRYST1 36.510 42.630 95.070 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 0.027390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023458 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010519 0.00000