HEADER VIRAL PROTEIN 21-NOV-14 4X0C TITLE CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN NSW0514 IN COMPLEX TITLE 2 WITH HBGA TYPE LEX (TRIGLYCAN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VP1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: P DOMAIN, UNP RESIDUES 225-530; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOROVIRUS HU/GII.4/SYDNEY/NSW0514/2012/AU; SOURCE 3 ORGANISM_TAXID: 1241973; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: MBP-HTSHP KEYWDS VIRAL CAPSID PROTEIN, PROTRUDING DOMAIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.K.SINGH,G.S.HANSMAN REVDAT 5 10-JAN-24 4X0C 1 HETSYN REVDAT 4 29-JUL-20 4X0C 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 04-MAR-15 4X0C 1 SHEET REVDAT 2 04-FEB-15 4X0C 1 JRNL REVDAT 1 17-DEC-14 4X0C 0 JRNL AUTH B.K.SINGH,M.M.LEUTHOLD,G.S.HANSMAN JRNL TITL HUMAN NOROVIRUSES' FONDNESS FOR HISTO-BLOOD GROUP ANTIGENS. JRNL REF J.VIROL. V. 89 2024 2015 JRNL REFN ESSN 1098-5514 JRNL PMID 25428879 JRNL DOI 10.1128/JVI.02968-14 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 112461 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5621 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 40.1400 - 5.3404 0.97 3788 201 0.1595 0.1645 REMARK 3 2 5.3404 - 4.2403 0.99 3690 194 0.1181 0.1335 REMARK 3 3 4.2403 - 3.7048 1.00 3665 192 0.1351 0.1477 REMARK 3 4 3.7048 - 3.3662 1.00 3633 191 0.1561 0.1971 REMARK 3 5 3.3662 - 3.1250 1.00 3625 190 0.1460 0.1671 REMARK 3 6 3.1250 - 2.9409 1.00 3608 190 0.1537 0.1593 REMARK 3 7 2.9409 - 2.7936 1.00 3584 188 0.1468 0.1702 REMARK 3 8 2.7936 - 2.6720 1.00 3611 190 0.1380 0.1587 REMARK 3 9 2.6720 - 2.5692 1.00 3568 188 0.1399 0.1796 REMARK 3 10 2.5692 - 2.4805 1.00 3578 187 0.1373 0.1556 REMARK 3 11 2.4805 - 2.4030 1.00 3573 188 0.1374 0.1606 REMARK 3 12 2.4030 - 2.3343 1.00 3550 187 0.1327 0.1652 REMARK 3 13 2.3343 - 2.2729 1.00 3553 187 0.1349 0.1590 REMARK 3 14 2.2729 - 2.2174 1.00 3559 188 0.1370 0.1494 REMARK 3 15 2.2174 - 2.1670 1.00 3563 187 0.1546 0.1700 REMARK 3 16 2.1670 - 2.1209 1.00 3534 186 0.1648 0.1913 REMARK 3 17 2.1209 - 2.0785 1.00 3546 187 0.1683 0.1914 REMARK 3 18 2.0785 - 2.0393 0.98 3490 184 0.2008 0.2200 REMARK 3 19 2.0393 - 2.0028 0.99 3501 184 0.1865 0.2103 REMARK 3 20 2.0028 - 1.9689 1.00 3531 186 0.1990 0.2098 REMARK 3 21 1.9689 - 1.9371 0.99 3521 185 0.1985 0.2265 REMARK 3 22 1.9371 - 1.9073 0.99 3513 185 0.2209 0.2540 REMARK 3 23 1.9073 - 1.8793 0.99 3513 185 0.2205 0.2508 REMARK 3 24 1.8793 - 1.8528 0.99 3529 186 0.2206 0.2539 REMARK 3 25 1.8528 - 1.8278 0.99 3524 184 0.2296 0.2120 REMARK 3 26 1.8278 - 1.8040 0.99 3485 184 0.2434 0.2564 REMARK 3 27 1.8040 - 1.7815 0.99 3532 186 0.2593 0.2850 REMARK 3 28 1.7815 - 1.7600 0.99 3492 184 0.2770 0.3024 REMARK 3 29 1.7600 - 1.7395 0.99 3487 183 0.2925 0.2935 REMARK 3 30 1.7395 - 1.7200 0.99 3494 184 0.2998 0.3208 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.16 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 : 0.011 5086 REMARK 3 ANGLE : 1.297 6938 REMARK 3 CHIRALITY : 0.054 784 REMARK 3 PLANARITY : 0.007 905 REMARK 3 DIHEDRAL : 12.462 1874 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 225 THROUGH 292 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.0945 23.0384 -24.4062 REMARK 3 T TENSOR REMARK 3 T11: 0.0969 T22: 0.1377 REMARK 3 T33: 0.1000 T12: 0.0146 REMARK 3 T13: 0.0089 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 1.6442 L22: 1.8944 REMARK 3 L33: 1.2079 L12: 0.0238 REMARK 3 L13: 0.2639 L23: 0.1129 REMARK 3 S TENSOR REMARK 3 S11: -0.0123 S12: -0.1389 S13: 0.0014 REMARK 3 S21: -0.0099 S22: 0.0136 S23: -0.0944 REMARK 3 S31: 0.1011 S32: 0.0121 S33: -0.0149 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 293 THROUGH 380 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.7427 41.1308 -22.7905 REMARK 3 T TENSOR REMARK 3 T11: 0.1292 T22: 0.2518 REMARK 3 T33: 0.2560 T12: 0.0744 REMARK 3 T13: -0.0035 T23: -0.0476 REMARK 3 L TENSOR REMARK 3 L11: 1.1557 L22: 2.5652 REMARK 3 L33: 0.7014 L12: 0.6967 REMARK 3 L13: 0.1599 L23: -0.4804 REMARK 3 S TENSOR REMARK 3 S11: -0.0556 S12: -0.0774 S13: 0.3405 REMARK 3 S21: 0.0303 S22: -0.0115 S23: 0.3523 REMARK 3 S31: -0.1318 S32: -0.3136 S33: 0.0181 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 381 THROUGH 530 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.6549 16.0914 -20.1734 REMARK 3 T TENSOR REMARK 3 T11: 0.1780 T22: 0.1677 REMARK 3 T33: 0.1673 T12: 0.0315 REMARK 3 T13: -0.0188 T23: 0.0425 REMARK 3 L TENSOR REMARK 3 L11: 0.9564 L22: 1.4855 REMARK 3 L33: 1.3579 L12: 0.4121 REMARK 3 L13: 0.3006 L23: 0.3880 REMARK 3 S TENSOR REMARK 3 S11: 0.1017 S12: -0.1681 S13: -0.1845 REMARK 3 S21: 0.1800 S22: -0.0330 S23: -0.1742 REMARK 3 S31: 0.3320 S32: 0.0280 S33: -0.0141 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 224 THROUGH 292 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.6230 36.8820 -32.8165 REMARK 3 T TENSOR REMARK 3 T11: 0.1074 T22: 0.1324 REMARK 3 T33: 0.1476 T12: 0.0297 REMARK 3 T13: -0.0132 T23: 0.0125 REMARK 3 L TENSOR REMARK 3 L11: 0.9071 L22: 0.4892 REMARK 3 L33: 1.9893 L12: 0.2336 REMARK 3 L13: 0.5001 L23: 0.3123 REMARK 3 S TENSOR REMARK 3 S11: -0.0203 S12: -0.0026 S13: 0.0180 REMARK 3 S21: -0.0048 S22: -0.0084 S23: -0.0453 REMARK 3 S31: -0.0475 S32: 0.0203 S33: 0.0307 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 293 THROUGH 352 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.4645 40.4840 -12.9479 REMARK 3 T TENSOR REMARK 3 T11: 0.1272 T22: 0.1493 REMARK 3 T33: 0.1304 T12: 0.0156 REMARK 3 T13: -0.0273 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: 2.4038 L22: 0.2562 REMARK 3 L33: 2.2845 L12: 0.4804 REMARK 3 L13: -0.4817 L23: -0.1785 REMARK 3 S TENSOR REMARK 3 S11: 0.0138 S12: -0.2458 S13: -0.0179 REMARK 3 S21: 0.0997 S22: -0.0796 S23: -0.0519 REMARK 3 S31: -0.0892 S32: 0.0414 S33: 0.0625 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 353 THROUGH 418 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.9239 48.1890 -18.1159 REMARK 3 T TENSOR REMARK 3 T11: 0.1701 T22: 0.1430 REMARK 3 T33: 0.1733 T12: 0.0156 REMARK 3 T13: -0.0330 T23: -0.0382 REMARK 3 L TENSOR REMARK 3 L11: 1.5012 L22: 1.0549 REMARK 3 L33: 2.1801 L12: 0.3568 REMARK 3 L13: -0.1166 L23: -0.5124 REMARK 3 S TENSOR REMARK 3 S11: 0.0268 S12: -0.2087 S13: 0.2355 REMARK 3 S21: 0.1257 S22: -0.0395 S23: 0.0385 REMARK 3 S31: -0.3361 S32: 0.0877 S33: -0.0028 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 419 THROUGH 530 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.9067 37.3232 -45.6678 REMARK 3 T TENSOR REMARK 3 T11: 0.1356 T22: 0.1745 REMARK 3 T33: 0.1420 T12: 0.0219 REMARK 3 T13: -0.0170 T23: 0.0287 REMARK 3 L TENSOR REMARK 3 L11: 0.6892 L22: 1.0314 REMARK 3 L33: 1.6403 L12: -0.0798 REMARK 3 L13: -0.0089 L23: 0.2783 REMARK 3 S TENSOR REMARK 3 S11: -0.0344 S12: 0.1522 S13: 0.0142 REMARK 3 S21: -0.1958 S22: -0.0147 S23: -0.0040 REMARK 3 S31: -0.0707 S32: 0.0683 S33: 0.0489 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 2783 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4X0C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000204859. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978196 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 116084 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 45.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 1.28600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.3 REMARK 200 STARTING MODEL: 4OOS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM FORMATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 95.50000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.41500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.41500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.75000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.41500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.41500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 143.25000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.41500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.41500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.75000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.41500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.41500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 143.25000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 95.50000 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: 7070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 SER A 224 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 ARG A 484 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 523 CG CD OE1 NE2 REMARK 470 ARG B 411 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 412 CG OD1 ND2 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 B 1065 O HOH B 1075 2.08 REMARK 500 O HOH A 1016 O HOH A 1019 2.13 REMARK 500 O HOH A 1002 O HOH A 1003 2.14 REMARK 500 O HOH B 1063 O HOH B 1080 2.15 REMARK 500 O HOH A 1000 O HOH A 1023 2.18 REMARK 500 O HOH B 1058 O HOH B 1060 2.18 REMARK 500 O HOH B 1019 O HOH B 1040 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 B 756 O HOH B 762 8554 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 SER A 254 24.88 -145.31 REMARK 500 GLN A 260 50.81 -143.29 REMARK 500 ARG A 373 -15.12 -153.87 REMARK 500 SER A 442 142.73 -178.43 REMARK 500 SER B 254 23.36 -143.53 REMARK 500 GLN B 260 50.73 -143.17 REMARK 500 ARG B 373 -16.37 -153.19 REMARK 500 SER B 442 143.95 -178.39 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 980 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH B1001 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B1034 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH B1036 DISTANCE = 7.10 ANGSTROMS REMARK 525 HOH B1049 DISTANCE = 5.87 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OOS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN NSW0514 REMARK 900 RELATED ID: 4WZT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN NSW0514 IN REMARK 900 COMPLEX WITH HBGA TYPE A (TRIGLYCAN) REMARK 900 RELATED ID: 4OP7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN NSW0514 IN REMARK 900 COMPLEX WITH HBGA TYPE B (TRIGLYCAN) DBREF 4X0C A 225 530 UNP K4LM89 K4LM89_9CALI 225 530 DBREF 4X0C B 225 530 UNP K4LM89 K4LM89_9CALI 225 530 SEQADV 4X0C SER A 224 UNP K4LM89 EXPRESSION TAG SEQADV 4X0C SER B 224 UNP K4LM89 EXPRESSION TAG SEQRES 1 A 307 SER LYS PRO PHE SER VAL PRO VAL LEU THR VAL GLU GLU SEQRES 2 A 307 MET THR ASN SER ARG PHE PRO ILE PRO LEU GLU LYS LEU SEQRES 3 A 307 PHE THR GLY PRO SER SER ALA PHE VAL VAL GLN PRO GLN SEQRES 4 A 307 ASN GLY ARG CYS THR THR ASP GLY VAL LEU LEU GLY THR SEQRES 5 A 307 THR GLN LEU SER PRO VAL ASN ILE CYS THR PHE ARG GLY SEQRES 6 A 307 ASP VAL THR HIS ILE THR GLY SER ARG ASN TYR THR MET SEQRES 7 A 307 ASN LEU ALA SER GLN ASN TRP ASN ASP TYR ASP PRO THR SEQRES 8 A 307 GLU GLU ILE PRO ALA PRO LEU GLY THR PRO ASP PHE VAL SEQRES 9 A 307 GLY LYS ILE GLN GLY VAL LEU THR GLN THR THR ARG THR SEQRES 10 A 307 ASP GLY SER THR ARG GLY HIS LYS ALA THR VAL TYR THR SEQRES 11 A 307 GLY SER ALA ASP PHE ALA PRO LYS LEU GLY ARG VAL GLN SEQRES 12 A 307 PHE GLU THR ASP THR ASP ARG ASP PHE GLU ALA ASN GLN SEQRES 13 A 307 ASN THR LYS PHE THR PRO VAL GLY VAL ILE GLN ASP GLY SEQRES 14 A 307 GLY THR THR HIS ARG ASN GLU PRO GLN GLN TRP VAL LEU SEQRES 15 A 307 PRO SER TYR SER GLY ARG ASN THR HIS ASN VAL HIS LEU SEQRES 16 A 307 ALA PRO ALA VAL ALA PRO THR PHE PRO GLY GLU GLN LEU SEQRES 17 A 307 LEU PHE PHE ARG SER THR MET PRO GLY CYS SER GLY TYR SEQRES 18 A 307 PRO ASN MET ASP LEU ASP CYS LEU LEU PRO GLN GLU TRP SEQRES 19 A 307 VAL GLN TYR PHE TYR GLN GLU ALA ALA PRO ALA GLN SER SEQRES 20 A 307 ASP VAL ALA LEU LEU ARG PHE VAL ASN PRO ASP THR GLY SEQRES 21 A 307 ARG VAL LEU PHE GLU CYS LYS LEU HIS LYS SER GLY TYR SEQRES 22 A 307 VAL THR VAL ALA HIS THR GLY GLN HIS ASP LEU VAL ILE SEQRES 23 A 307 PRO PRO ASN GLY TYR PHE ARG PHE ASP SER TRP VAL ASN SEQRES 24 A 307 GLN PHE TYR THR LEU ALA PRO MET SEQRES 1 B 307 SER LYS PRO PHE SER VAL PRO VAL LEU THR VAL GLU GLU SEQRES 2 B 307 MET THR ASN SER ARG PHE PRO ILE PRO LEU GLU LYS LEU SEQRES 3 B 307 PHE THR GLY PRO SER SER ALA PHE VAL VAL GLN PRO GLN SEQRES 4 B 307 ASN GLY ARG CYS THR THR ASP GLY VAL LEU LEU GLY THR SEQRES 5 B 307 THR GLN LEU SER PRO VAL ASN ILE CYS THR PHE ARG GLY SEQRES 6 B 307 ASP VAL THR HIS ILE THR GLY SER ARG ASN TYR THR MET SEQRES 7 B 307 ASN LEU ALA SER GLN ASN TRP ASN ASP TYR ASP PRO THR SEQRES 8 B 307 GLU GLU ILE PRO ALA PRO LEU GLY THR PRO ASP PHE VAL SEQRES 9 B 307 GLY LYS ILE GLN GLY VAL LEU THR GLN THR THR ARG THR SEQRES 10 B 307 ASP GLY SER THR ARG GLY HIS LYS ALA THR VAL TYR THR SEQRES 11 B 307 GLY SER ALA ASP PHE ALA PRO LYS LEU GLY ARG VAL GLN SEQRES 12 B 307 PHE GLU THR ASP THR ASP ARG ASP PHE GLU ALA ASN GLN SEQRES 13 B 307 ASN THR LYS PHE THR PRO VAL GLY VAL ILE GLN ASP GLY SEQRES 14 B 307 GLY THR THR HIS ARG ASN GLU PRO GLN GLN TRP VAL LEU SEQRES 15 B 307 PRO SER TYR SER GLY ARG ASN THR HIS ASN VAL HIS LEU SEQRES 16 B 307 ALA PRO ALA VAL ALA PRO THR PHE PRO GLY GLU GLN LEU SEQRES 17 B 307 LEU PHE PHE ARG SER THR MET PRO GLY CYS SER GLY TYR SEQRES 18 B 307 PRO ASN MET ASP LEU ASP CYS LEU LEU PRO GLN GLU TRP SEQRES 19 B 307 VAL GLN TYR PHE TYR GLN GLU ALA ALA PRO ALA GLN SER SEQRES 20 B 307 ASP VAL ALA LEU LEU ARG PHE VAL ASN PRO ASP THR GLY SEQRES 21 B 307 ARG VAL LEU PHE GLU CYS LYS LEU HIS LYS SER GLY TYR SEQRES 22 B 307 VAL THR VAL ALA HIS THR GLY GLN HIS ASP LEU VAL ILE SEQRES 23 B 307 PRO PRO ASN GLY TYR PHE ARG PHE ASP SER TRP VAL ASN SEQRES 24 B 307 GLN PHE TYR THR LEU ALA PRO MET HET NDG C 1 30 HET FUC C 2 20 HET GAL C 3 22 HET NDG D 1 15 HET FUC D 2 10 HET GAL D 3 11 HET EDO A 601 4 HET EDO A 602 4 HET FMT A 603 3 HET EDO B 601 4 HET EDO B 602 4 HET FMT B 603 3 HET FMT B 604 3 HET FMT B 605 3 HET FMT B 606 3 HET FMT B 607 3 HETNAM NDG 2-ACETAMIDO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL HETNAM FMT FORMIC ACID HETSYN NDG N-ACETYL-ALPHA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 NDG ALPHA-D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2- HETSYN 3 NDG ACETAMIDO-2-DEOXY-GLUCOSE; 2-(ACETYLAMINO)-2-DEOXY-A- HETSYN 4 NDG D-GLUCOPYRANOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 NDG 2(C8 H15 N O6) FORMUL 3 FUC 2(C6 H12 O5) FORMUL 3 GAL 2(C6 H12 O6) FORMUL 5 EDO 4(C2 H6 O2) FORMUL 7 FMT 6(C H2 O2) FORMUL 15 HOH *747(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 HELIX 5 AA5 THR B 233 MET B 237 5 5 HELIX 6 AA6 ALA B 359 LEU B 362 5 4 HELIX 7 AA7 PRO B 454 ALA B 465 1 12 SHEET 1 1 1 LYS A 248 THR A 251 0 SHEET 1 2 1 PHE A 286 ILE A 293 0 SHEET 1 3 1 ASN A 298 LEU A 303 0 SHEET 1 4 1 LYS A 329 THR A 337 0 SHEET 1 5 1 THR A 344 TYR A 352 0 SHEET 1 6 1 ARG A 364 THR A 369 0 SHEET 1 7 1 THR A 381 ILE A 389 0 SHEET 1 8 1 GLU A 429 THR A 437 0 SHEET 1 9 1 GLY A 440 GLY A 443 0 SHEET 1 10 1 ASP A 448 CYS A 451 0 SHEET 1 11 1 VAL A 472 VAL A 478 0 SHEET 1 12 1 VAL A 485 HIS A 492 0 SHEET 1 13 1 TYR A 496 ALA A 500 0 SHEET 1 14 1 HIS A 505 ASP A 506 0 SHEET 1 15 1 TYR A 514 VAL A 521 0 SHEET 1 16 1 LYS B 248 GLY B 252 0 SHEET 1 17 1 PHE B 286 HIS B 292 0 SHEET 1 18 1 ASN B 298 LEU B 303 0 SHEET 1 19 1 LYS B 329 THR B 337 0 SHEET 1 20 1 THR B 344 TYR B 352 0 SHEET 1 21 1 ARG B 364 THR B 369 0 SHEET 1 22 1 THR B 381 ILE B 389 0 SHEET 1 23 1 GLU B 429 THR B 437 0 SHEET 1 24 1 GLY B 440 GLY B 443 0 SHEET 1 25 1 ASP B 448 CYS B 451 0 SHEET 1 26 1 VAL B 472 ASN B 479 0 SHEET 1 27 1 ARG B 484 HIS B 492 0 SHEET 1 28 1 TYR B 496 ALA B 500 0 SHEET 1 29 1 HIS B 505 ASP B 506 0 SHEET 1 30 1 TYR B 514 VAL B 521 0 LINK O3 BNDG C 1 C1 BFUC C 2 1555 1555 1.40 LINK O4 ANDG C 1 C1 AGAL C 3 1555 1555 1.44 LINK O4 BNDG C 1 C1 BGAL C 3 1555 1555 1.44 LINK O3 NDG D 1 C1 FUC D 2 1555 1555 1.44 LINK O4 NDG D 1 C1 GAL D 3 1555 1555 1.40 CISPEP 1 GLU A 399 PRO A 400 0 -7.85 CISPEP 2 GLU B 399 PRO B 400 0 -7.83 CRYST1 104.830 104.830 191.000 90.00 90.00 90.00 P 41 21 2 16 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 0.009539 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009539 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005236 0.00000