HEADER VIRAL PROTEIN 23-MAY-17 5VX4 TITLE VP8* OF A G2P[4] HUMAN ROTAVIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER CAPSID PROTEIN VP4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 54-213; COMPND 5 SYNONYM: INDIAN G2P[4] ROTAVIRUS VP8*; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ROTAVIRUS A; SOURCE 3 ORGANISM_TAXID: 28875; 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 3 04-OCT-23 5VX4 1 REMARK REVDAT 2 11-DEC-19 5VX4 1 REMARK REVDAT 1 18-JUL-18 5VX4 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. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.280 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 19625 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1005 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 34.2736 - 3.7342 0.98 2701 145 0.1389 0.1898 REMARK 3 2 3.7342 - 2.9645 0.93 2545 143 0.1574 0.1940 REMARK 3 3 2.9645 - 2.5899 0.95 2619 143 0.1766 0.2644 REMARK 3 4 2.5899 - 2.3532 0.96 2645 124 0.1854 0.2538 REMARK 3 5 2.3532 - 2.1845 0.95 2651 121 0.1763 0.1905 REMARK 3 6 2.1845 - 2.0558 0.95 2607 147 0.1718 0.2465 REMARK 3 7 2.0558 - 1.9528 0.95 2578 155 0.1676 0.1869 REMARK 3 8 1.9528 - 1.8678 0.95 2623 140 0.1731 0.2396 REMARK 3 9 1.8678 - 1.7959 0.94 2614 122 0.1764 0.2184 REMARK 3 10 1.7959 - 1.7340 0.93 2559 151 0.1884 0.2235 REMARK 3 11 1.7340 - 1.6797 0.92 2541 131 0.2046 0.2455 REMARK 3 12 1.6797 - 1.6317 0.92 2492 163 0.2045 0.2520 REMARK 3 13 1.6317 - 1.5888 0.91 2532 149 0.2000 0.2308 REMARK 3 14 1.5888 - 1.5500 0.91 2532 119 0.2086 0.2745 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.560 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 1364 REMARK 3 ANGLE : 1.050 1857 REMARK 3 CHIRALITY : 0.039 196 REMARK 3 PLANARITY : 0.005 243 REMARK 3 DIHEDRAL : 12.900 496 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 5VX4 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_1000228093. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9774 REMARK 200 MONOCHROMATOR : SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R 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 : 19627 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 31.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.02462 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 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) : 0.22800 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 (%): 37.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE, PH 9.0, 30% REMARK 280 W/V PEG6000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 28.29500 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 TOTAL BURIED SURFACE AREA: 280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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 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 OD1 ASN A 189 O HOH A 401 2.11 REMARK 500 O HOH A 411 O HOH A 563 2.14 REMARK 500 O HOH A 436 O HOH A 594 2.14 REMARK 500 O HOH A 403 O HOH A 533 2.14 REMARK 500 O HOH A 442 O HOH A 474 2.17 REMARK 500 O HOH A 401 O HOH A 552 2.19 REMARK 500 O HOH A 654 O HOH A 665 2.19 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 590 O HOH A 609 1655 2.18 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 SER A 99 -62.69 -135.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 301 DBREF 5VX4 A 64 223 UNP Q2VE61 Q2VE61_9REOV 54 213 SEQADV 5VX4 GLY A 62 UNP Q2VE61 EXPRESSION TAG SEQADV 5VX4 SER A 63 UNP Q2VE61 EXPRESSION TAG SEQRES 1 A 162 GLY SER ILE LEU ASP GLY PRO TYR GLN PRO THR THR PHE SEQRES 2 A 162 LYS PRO PRO ASN ASP TYR TRP LEU LEU ILE SER SER ASN SEQRES 3 A 162 THR ASP GLY VAL VAL TYR GLU SER THR ASN ASN SER ASP SEQRES 4 A 162 PHE TRP THR ALA VAL ILE ALA VAL GLU PRO HIS VAL SER SEQRES 5 A 162 GLN THR ASN ARG GLN TYR VAL LEU PHE GLY GLU ASN LYS SEQRES 6 A 162 GLN PHE ASN VAL GLU ASN SER SER ASP LYS TRP LYS PHE SEQRES 7 A 162 PHE GLU MET PHE LYS GLY SER SER GLN SER ASP PHE SER SEQRES 8 A 162 ASN ARG ARG THR LEU THR SER ASN ASN ARG LEU VAL GLY SEQRES 9 A 162 MET LEU LYS TYR GLY GLY ARG VAL TRP THR PHE HIS GLY SEQRES 10 A 162 GLU THR PRO ARG ALA THR THR ASP SER SER ASN THR ALA SEQRES 11 A 162 ASP LEU ASN ASN ILE SER ILE ILE ILE HIS SER GLU PHE SEQRES 12 A 162 TYR ILE ILE PRO ARG SER GLN GLU SER LYS CYS ASN GLU SEQRES 13 A 162 TYR ILE ASN ASN GLY LEU HET TRS A 301 8 HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 TRS C4 H12 N O3 1+ FORMUL 3 HOH *274(H2 O) HELIX 1 AA1 GLN A 211 GLY A 222 1 12 SHEET 1 AA111 ASP A 66 TYR A 69 0 SHEET 2 AA111 PHE A 204 PRO A 208 -1 O PHE A 204 N TYR A 69 SHEET 3 AA111 TYR A 80 SER A 85 -1 N TRP A 81 O ILE A 207 SHEET 4 AA111 LEU A 163 TYR A 169 -1 O MET A 166 N LEU A 82 SHEET 5 AA111 ARG A 172 GLU A 179 -1 O TRP A 174 N LEU A 167 SHEET 6 AA111 SER A 152 THR A 158 1 N THR A 156 O GLY A 178 SHEET 7 AA111 LYS A 138 LYS A 144 -1 N PHE A 143 O SER A 152 SHEET 8 AA111 TRP A 102 VAL A 108 -1 N ALA A 104 O MET A 142 SHEET 9 AA111 GLY A 90 THR A 96 -1 N VAL A 92 O VAL A 105 SHEET 10 AA111 SER A 197 ILE A 200 -1 O SER A 197 N THR A 96 SHEET 11 AA111 THR A 72 PHE A 74 -1 N PHE A 74 O ILE A 198 SHEET 1 AA2 6 ASP A 66 TYR A 69 0 SHEET 2 AA2 6 PHE A 204 PRO A 208 -1 O PHE A 204 N TYR A 69 SHEET 3 AA2 6 TYR A 80 SER A 85 -1 N TRP A 81 O ILE A 207 SHEET 4 AA2 6 LEU A 163 TYR A 169 -1 O MET A 166 N LEU A 82 SHEET 5 AA2 6 ARG A 172 GLU A 179 -1 O TRP A 174 N LEU A 167 SHEET 6 AA2 6 THR A 184 ASN 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 VAL A 130 N THR A 115 CISPEP 1 GLY A 67 PRO A 68 0 0.60 CISPEP 2 THR A 180 PRO A 181 0 7.08 SITE 1 AC1 6 TYR A 169 THR A 185 ARG A 209 GLU A 212 SITE 2 AC1 6 HOH A 531 HOH A 548 CRYST1 34.330 56.590 37.310 90.00 93.52 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 0.029129 0.000000 0.001792 0.00000 SCALE2 0.000000 0.017671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026853 0.00000