HEADER VIRAL PROTEIN 01-FEB-24 8Y5V TITLE GII.4 SYDNEY PD AND 2'-FL COMPND MOL_ID: 1; COMPND 2 MOLECULE: GII.4 SYDNEY PD IN COMPLEX WITH 2'-FL (POWDER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE GENEBANK ACCESSION NUMBER IS JX459908 FOR THIS COMPND 6 PROTEIN. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOROVIRUS; SOURCE 3 ORGANISM_TAXID: 142786; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SUGAR, COMPLEX, MILK OLIGOSACCHARIDE, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.HANSMAN,J.R.H.TAME,G.KHER,M.PANCERA REVDAT 1 19-JUN-24 8Y5V 0 JRNL AUTH G.HANSMAN,J.R.H.TAME,G.KHER,M.PANCERA JRNL TITL GII.4 SYDNEY PD AND 2'-FL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 42174 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2107 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 41.6900 - 3.7900 0.98 2827 150 0.1384 0.1542 REMARK 3 2 3.7900 - 3.0100 0.92 2629 137 0.1413 0.1591 REMARK 3 3 3.0100 - 2.6300 0.97 2735 147 0.1470 0.1912 REMARK 3 4 2.6300 - 2.3900 0.97 2745 142 0.1485 0.1812 REMARK 3 5 2.3900 - 2.2200 0.97 2729 149 0.1408 0.1995 REMARK 3 6 2.2200 - 2.0900 0.97 2751 142 0.1443 0.1721 REMARK 3 7 2.0900 - 1.9800 0.91 2539 138 0.1528 0.1571 REMARK 3 8 1.9800 - 1.9000 0.93 2623 136 0.1606 0.1899 REMARK 3 9 1.9000 - 1.8200 0.95 2654 141 0.1617 0.1937 REMARK 3 10 1.8200 - 1.7600 0.96 2663 145 0.1689 0.2179 REMARK 3 11 1.7600 - 1.7100 0.96 2703 140 0.1816 0.2270 REMARK 3 12 1.7100 - 1.6600 0.95 2676 129 0.1992 0.2427 REMARK 3 13 1.6600 - 1.6100 0.95 2656 148 0.2178 0.2677 REMARK 3 14 1.6100 - 1.5700 0.95 2678 147 0.2374 0.2633 REMARK 3 15 1.5700 - 1.5400 0.88 2459 116 0.2697 0.2976 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 17.860 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 : 0.009 2491 REMARK 3 ANGLE : 1.065 3402 REMARK 3 CHIRALITY : 0.227 386 REMARK 3 PLANARITY : 0.011 444 REMARK 3 DIHEDRAL : 13.360 896 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 8Y5V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300044630. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95372 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42181 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 47.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.96000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM FORMATE, 20% PEG 3350, PH REMARK 280 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 49.31200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.88150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.31200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.88150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 197.24800 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 THR A 222 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 224 OG REMARK 470 GLU A 315 CG CD OE1 OE2 REMARK 470 ARG A 339 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 366 CG CD OE1 NE2 REMARK 470 GLU A 368 CG CD OE1 OE2 REMARK 470 ARG A 373 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 398 CG OD1 ND2 REMARK 470 GLN A 523 CG CD OE1 NE2 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 GLN A 260 49.60 -141.17 REMARK 500 ARG A 373 -25.15 -148.04 REMARK 500 ASP A 374 35.83 -99.52 REMARK 500 VAL A 386 -51.45 -122.05 REMARK 500 ASP A 391 -161.09 -177.45 REMARK 500 SER A 442 140.42 176.59 REMARK 500 REMARK 500 REMARK: NULL DBREF 8Y5V A 222 530 PDB 8Y5V 8Y5V 222 530 SEQRES 1 A 309 THR GLY SER LYS PRO PHE SER VAL PRO VAL LEU THR VAL SEQRES 2 A 309 GLU GLU MET THR ASN SER ARG PHE PRO ILE PRO LEU GLU SEQRES 3 A 309 LYS LEU PHE THR GLY PRO SER SER ALA PHE VAL VAL GLN SEQRES 4 A 309 PRO GLN ASN GLY ARG CYS THR THR ASP GLY VAL LEU LEU SEQRES 5 A 309 GLY THR THR GLN LEU SER PRO VAL ASN ILE CYS THR PHE SEQRES 6 A 309 ARG GLY ASP VAL THR HIS ILE THR GLY SER ARG ASN TYR SEQRES 7 A 309 THR MET ASN LEU ALA SER GLN ASN TRP ASN ASP TYR ASP SEQRES 8 A 309 PRO THR GLU GLU ILE PRO ALA PRO LEU GLY THR PRO ASP SEQRES 9 A 309 PHE VAL GLY LYS ILE GLN GLY VAL LEU THR GLN THR THR SEQRES 10 A 309 ARG THR ASP GLY SER THR ARG GLY HIS LYS ALA THR VAL SEQRES 11 A 309 TYR THR GLY SER ALA ASP PHE ALA PRO LYS LEU GLY ARG SEQRES 12 A 309 VAL GLN PHE GLU THR ASP THR ASP ARG ASP PHE GLU ALA SEQRES 13 A 309 ASN GLN ASN THR LYS PHE THR PRO VAL GLY VAL ILE GLN SEQRES 14 A 309 ASP GLY GLY THR THR HIS ARG ASN GLU PRO GLN GLN TRP SEQRES 15 A 309 VAL LEU PRO SER TYR SER GLY ARG ASN THR HIS ASN VAL SEQRES 16 A 309 HIS LEU ALA PRO ALA VAL ALA PRO THR PHE PRO GLY GLU SEQRES 17 A 309 GLN LEU LEU PHE PHE ARG SER THR MET PRO GLY CYS SER SEQRES 18 A 309 GLY TYR PRO ASN MET ASP LEU ASP CYS LEU LEU PRO GLN SEQRES 19 A 309 GLU TRP VAL GLN TYR PHE TYR GLN GLU ALA ALA PRO ALA SEQRES 20 A 309 GLN SER ASP VAL ALA LEU LEU ARG PHE VAL ASN PRO ASP SEQRES 21 A 309 THR GLY ARG VAL LEU PHE GLU CYS LYS LEU HIS LYS SER SEQRES 22 A 309 GLY TYR VAL THR VAL ALA HIS THR GLY GLN HIS ASP LEU SEQRES 23 A 309 VAL ILE PRO PRO ASN GLY TYR PHE ARG PHE ASP SER TRP SEQRES 24 A 309 VAL ASN GLN PHE TYR THR LEU ALA PRO MET HET GLC C 1 12 HET GAL C 2 11 HET FUC C 3 10 HET EDO A 601 4 HET EDO A 602 4 HET EDO A 603 4 HET EDO A 604 4 HET EDO A 605 10 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GLC C6 H12 O6 FORMUL 2 GAL C6 H12 O6 FORMUL 2 FUC C6 H12 O5 FORMUL 3 EDO 5(C2 H6 O2) FORMUL 8 HOH *340(H2 O) HELIX 1 AA1 THR A 233 MET A 237 5 5 HELIX 2 AA2 SER A 279 ILE A 283 5 5 HELIX 3 AA3 ALA A 359 LEU A 362 5 4 HELIX 4 AA4 PRO A 454 ALA A 465 1 12 SHEET 1 AA1 4 ASP A 448 CYS A 451 0 SHEET 2 AA1 4 GLU A 429 THR A 437 -1 N PHE A 434 O CYS A 451 SHEET 3 AA1 4 LYS A 248 GLY A 252 -1 N PHE A 250 O PHE A 433 SHEET 4 AA1 4 HIS A 505 ASP A 506 -1 O HIS A 505 N THR A 251 SHEET 1 AA2 6 ASP A 448 CYS A 451 0 SHEET 2 AA2 6 GLU A 429 THR A 437 -1 N PHE A 434 O CYS A 451 SHEET 3 AA2 6 TYR A 496 ALA A 500 -1 O VAL A 499 N GLN A 430 SHEET 4 AA2 6 VAL A 485 HIS A 492 -1 N HIS A 492 O TYR A 496 SHEET 5 AA2 6 VAL A 472 VAL A 478 -1 N ALA A 473 O LEU A 491 SHEET 6 AA2 6 TYR A 514 VAL A 521 -1 O SER A 519 N LEU A 474 SHEET 1 AA3 8 GLY A 440 SER A 442 0 SHEET 2 AA3 8 THR A 381 ILE A 389 1 N VAL A 388 O CYS A 441 SHEET 3 AA3 8 LYS A 329 THR A 337 -1 N THR A 335 O LYS A 382 SHEET 4 AA3 8 THR A 344 TYR A 352 -1 O ALA A 349 N GLY A 332 SHEET 5 AA3 8 ARG A 364 THR A 369 -1 O GLU A 368 N THR A 350 SHEET 6 AA3 8 ASN A 298 LEU A 303 -1 N MET A 301 O VAL A 365 SHEET 7 AA3 8 PHE A 286 HIS A 292 -1 N THR A 291 O THR A 300 SHEET 8 AA3 8 THR A 381 ILE A 389 -1 O PHE A 383 N PHE A 286 LINK O4 GLC C 1 C1 GAL C 2 1555 1555 1.43 LINK O2 GAL C 2 C1 FUC C 3 1555 1555 1.45 CISPEP 1 GLU A 399 PRO A 400 0 -10.80 CRYST1 98.624 55.763 63.613 90.00 120.14 90.00 C 1 2 1 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 0.010140 0.000000 0.005887 0.00000 SCALE2 0.000000 0.017933 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018177 0.00000