HEADER VIRAL PROTEIN 20-NOV-14 4X06 TITLE CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4 IN COMPLEX TITLE 2 WITH HBGA TYPE B (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/SAGA4/2006/JP; SOURCE 3 ORGANISM_TAXID: 546981; 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 4 29-JUL-20 4X06 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 04-MAR-15 4X06 1 SHEET REVDAT 2 04-FEB-15 4X06 1 JRNL REVDAT 1 17-DEC-14 4X06 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. 1.22 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) : 1.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 176446 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.161 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 8823 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 32.3345 - 3.7832 0.95 5653 298 0.1570 0.1675 REMARK 3 2 3.7832 - 3.0035 0.97 5712 301 0.1401 0.1520 REMARK 3 3 3.0035 - 2.6240 0.95 5509 290 0.1481 0.1638 REMARK 3 4 2.6240 - 2.3842 0.97 5606 295 0.1363 0.1500 REMARK 3 5 2.3842 - 2.2134 0.97 5623 296 0.1240 0.1500 REMARK 3 6 2.2134 - 2.0829 0.97 5618 295 0.1244 0.1395 REMARK 3 7 2.0829 - 1.9786 0.96 5579 294 0.1215 0.1472 REMARK 3 8 1.9786 - 1.8925 0.96 5538 291 0.1247 0.1647 REMARK 3 9 1.8925 - 1.8196 0.97 5638 297 0.1212 0.1557 REMARK 3 10 1.8196 - 1.7568 0.98 5660 298 0.1147 0.1455 REMARK 3 11 1.7568 - 1.7019 0.98 5658 298 0.1156 0.1576 REMARK 3 12 1.7019 - 1.6533 0.98 5612 295 0.1148 0.1602 REMARK 3 13 1.6533 - 1.6097 0.98 5664 298 0.1102 0.1620 REMARK 3 14 1.6097 - 1.5705 0.96 5564 293 0.1132 0.1579 REMARK 3 15 1.5705 - 1.5348 0.97 5563 293 0.1123 0.1659 REMARK 3 16 1.5348 - 1.5021 0.98 5622 296 0.1131 0.1596 REMARK 3 17 1.5021 - 1.4721 0.98 5656 298 0.1145 0.1551 REMARK 3 18 1.4721 - 1.4443 0.98 5656 297 0.1171 0.1458 REMARK 3 19 1.4443 - 1.4185 0.98 5647 298 0.1221 0.1662 REMARK 3 20 1.4185 - 1.3944 0.98 5619 295 0.1245 0.1713 REMARK 3 21 1.3944 - 1.3719 0.98 5683 299 0.1294 0.1926 REMARK 3 22 1.3719 - 1.3508 0.97 5539 292 0.1326 0.1804 REMARK 3 23 1.3508 - 1.3310 0.98 5596 294 0.1337 0.1913 REMARK 3 24 1.3310 - 1.3122 0.98 5643 297 0.1475 0.2102 REMARK 3 25 1.3122 - 1.2945 0.98 5680 299 0.1579 0.2081 REMARK 3 26 1.2945 - 1.2777 0.98 5603 295 0.1557 0.1867 REMARK 3 27 1.2777 - 1.2617 0.98 5620 296 0.1564 0.2083 REMARK 3 28 1.2617 - 1.2465 0.97 5602 295 0.1613 0.2200 REMARK 3 29 1.2465 - 1.2320 0.97 5557 292 0.1718 0.2232 REMARK 3 30 1.2320 - 1.2182 0.82 4703 248 0.1848 0.2265 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.94 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 5184 REMARK 3 ANGLE : 1.357 7102 REMARK 3 CHIRALITY : 0.087 777 REMARK 3 PLANARITY : 0.008 925 REMARK 3 DIHEDRAL : 12.507 2004 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 4X06 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_1000204852. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97248 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 176472 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.220 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.540 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, PH 6.9, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 56.91500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.32500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.91500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.32500 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 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: 5810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 7.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 776 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 776 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 779 LIES ON A SPECIAL POSITION. 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 THR A 222 OG1 CG2 REMARK 470 GLU A 315 CG CD OE1 OE2 REMARK 470 GLU A 372 CG CD OE1 OE2 REMARK 470 THR A 394 OG1 CG2 REMARK 470 ASN B 307 CG OD1 ND2 REMARK 470 GLU B 315 CG CD OE1 OE2 REMARK 470 GLU B 372 CG CD OE1 OE2 REMARK 470 THR B 394 OG1 CG2 REMARK 470 ARG B 397 NE CZ NH1 NH2 REMARK 470 ARG B 411 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 523 CG CD OE1 NE2 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 HD22 ASN A 310 O HOH A 701 1.27 REMARK 500 HZ3 LYS B 329 OD1 ASP B 391 1.51 REMARK 500 OD1 ASN A 282 O HOH A 1028 1.89 REMARK 500 ND2 ASN A 310 O HOH A 701 2.17 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 HB3 HIS A 378 HD21 ASN B 479 4955 1.31 REMARK 500 O HOH B 749 O HOH B 755 21056 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 236 CD GLU B 236 OE1 -0.073 REMARK 500 SER B 254 CB SER B 254 OG -0.079 REMARK 500 ASN B 302 CA ASN B 302 C 0.163 REMARK 500 GLU B 488 CD GLU B 488 OE1 -0.067 REMARK 500 SER B 519 CB SER B 519 OG -0.080 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASN A 282 O - C - N ANGL. DEV. = -12.8 DEGREES REMARK 500 ARG A 297 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 SER A 393 N - CA - C ANGL. DEV. = 17.5 DEGREES REMARK 500 THR A 394 N - CA - C ANGL. DEV. = 24.5 DEGREES REMARK 500 ARG A 397 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 397 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG A 411 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASN A 512 N - CA - C ANGL. DEV. = 16.8 DEGREES REMARK 500 ASN A 512 CA - C - O ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG B 241 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 LEU B 306 CB - CG - CD2 ANGL. DEV. = 12.9 DEGREES REMARK 500 ASP B 312 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES 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 GLN A 260 49.60 -140.85 REMARK 500 ASN A 373 -4.36 -146.32 REMARK 500 THR A 394 -7.71 129.67 REMARK 500 SER A 442 146.41 -175.79 REMARK 500 VAL A 521 -166.66 -127.54 REMARK 500 GLN B 260 51.32 -142.66 REMARK 500 ASN B 373 -8.51 -142.66 REMARK 500 SER B 393 -93.62 6.44 REMARK 500 THR B 394 -67.45 161.68 REMARK 500 SER B 442 148.78 -179.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN A 390 ASP A 391 -148.08 REMARK 500 SER A 393 THR A 394 143.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN A 282 -25.04 REMARK 500 THR A 394 -12.26 REMARK 500 ASN B 282 11.15 REMARK 500 ASN B 282 -16.31 REMARK 500 THR B 394 -10.35 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 918 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A1014 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A1042 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH B1028 DISTANCE = 6.48 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OOX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4 REMARK 900 RELATED ID: 4WZK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4 IN REMARK 900 COMPLEX WITH HBGA TYPE H2 (TRIGLYCAN) REMARK 900 RELATED ID: 4WZE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4 IN REMARK 900 COMPLEX WITH HBGA TYPE LEY (TETRAGLYCAN) REMARK 900 RELATED ID: 4WZL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4 IN REMARK 900 COMPLEX WITH HBGA TYPE LEA (TRIGLYCAN) DBREF 4X06 A 225 530 UNP B5BTR7 B5BTR7_9CALI 225 530 DBREF 4X06 B 225 530 UNP B5BTR7 B5BTR7_9CALI 225 530 SEQADV 4X06 THR A 222 UNP B5BTR7 EXPRESSION TAG SEQADV 4X06 GLY A 223 UNP B5BTR7 EXPRESSION TAG SEQADV 4X06 SER A 224 UNP B5BTR7 EXPRESSION TAG SEQADV 4X06 THR B 222 UNP B5BTR7 EXPRESSION TAG SEQADV 4X06 GLY B 223 UNP B5BTR7 EXPRESSION TAG SEQADV 4X06 SER B 224 UNP B5BTR7 EXPRESSION TAG SEQRES 1 A 309 THR GLY SER LYS PRO PHE THR VAL PRO ILE 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 GLY 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 ALA GLY SER ARG ASN TYR SEQRES 7 A 309 THR MET ASN LEU ALA SER LEU ASN TRP ASN ASN 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 LEU LEU THR GLN THR THR SEQRES 10 A 309 LYS GLY ASP GLY SER THR ARG GLY HIS LYS ALA THR VAL SEQRES 11 A 309 TYR THR GLY SER ALA PRO PHE THR PRO LYS LEU GLY SER SEQRES 12 A 309 VAL GLN PHE SER THR ASP THR GLU ASN ASP PHE GLU THR SEQRES 13 A 309 HIS GLN ASN THR LYS PHE THR PRO VAL GLY VAL ILE GLN SEQRES 14 A 309 ASP GLY SER THR THR HIS ARG ASN GLU PRO GLN GLN TRP SEQRES 15 A 309 VAL LEU PRO SER TYR SER GLY ARG ASN VAL 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 HIS 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 SEQRES 1 B 309 THR GLY SER LYS PRO PHE THR VAL PRO ILE LEU THR VAL SEQRES 2 B 309 GLU GLU MET THR ASN SER ARG PHE PRO ILE PRO LEU GLU SEQRES 3 B 309 LYS LEU PHE THR GLY PRO SER GLY ALA PHE VAL VAL GLN SEQRES 4 B 309 PRO GLN ASN GLY ARG CYS THR THR ASP GLY VAL LEU LEU SEQRES 5 B 309 GLY THR THR GLN LEU SER PRO VAL ASN ILE CYS THR PHE SEQRES 6 B 309 ARG GLY ASP VAL THR HIS ILE ALA GLY SER ARG ASN TYR SEQRES 7 B 309 THR MET ASN LEU ALA SER LEU ASN TRP ASN ASN TYR ASP SEQRES 8 B 309 PRO THR GLU GLU ILE PRO ALA PRO LEU GLY THR PRO ASP SEQRES 9 B 309 PHE VAL GLY LYS ILE GLN GLY LEU LEU THR GLN THR THR SEQRES 10 B 309 LYS GLY ASP GLY SER THR ARG GLY HIS LYS ALA THR VAL SEQRES 11 B 309 TYR THR GLY SER ALA PRO PHE THR PRO LYS LEU GLY SER SEQRES 12 B 309 VAL GLN PHE SER THR ASP THR GLU ASN ASP PHE GLU THR SEQRES 13 B 309 HIS GLN ASN THR LYS PHE THR PRO VAL GLY VAL ILE GLN SEQRES 14 B 309 ASP GLY SER THR THR HIS ARG ASN GLU PRO GLN GLN TRP SEQRES 15 B 309 VAL LEU PRO SER TYR SER GLY ARG ASN VAL HIS ASN VAL SEQRES 16 B 309 HIS LEU ALA PRO ALA VAL ALA PRO THR PHE PRO GLY GLU SEQRES 17 B 309 GLN LEU LEU PHE PHE ARG SER THR MET PRO GLY CYS SER SEQRES 18 B 309 GLY TYR PRO ASN MET ASP LEU ASP CYS LEU LEU PRO GLN SEQRES 19 B 309 GLU TRP VAL GLN HIS PHE TYR GLN GLU ALA ALA PRO ALA SEQRES 20 B 309 GLN SER ASP VAL ALA LEU LEU ARG PHE VAL ASN PRO ASP SEQRES 21 B 309 THR GLY ARG VAL LEU PHE GLU CYS LYS LEU HIS LYS SER SEQRES 22 B 309 GLY TYR VAL THR VAL ALA HIS THR GLY GLN HIS ASP LEU SEQRES 23 B 309 VAL ILE PRO PRO ASN GLY TYR PHE ARG PHE ASP SER TRP SEQRES 24 B 309 VAL ASN GLN PHE TYR THR LEU ALA PRO MET HET GLA C 1 24 HET FUC C 2 20 HET GLA C 3 22 HET GLA D 1 24 HET FUC D 2 20 HET GLA D 3 22 HET ACT A 604 4 HET ACT B 604 4 HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM ACT ACETATE ION FORMUL 3 GLA 4(C6 H12 O6) FORMUL 3 FUC 2(C6 H12 O5) FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 7 HOH *716(H2 O) HELIX 1 AA1 THR A 233 MET A 237 5 5 HELIX 2 AA2 THR A 359 LEU A 362 5 4 HELIX 3 AA3 PRO A 454 ALA A 465 1 12 HELIX 4 AA4 THR B 233 MET B 237 5 5 HELIX 5 AA5 THR B 359 LEU B 362 5 4 HELIX 6 AA6 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 HIS A 292 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 SER 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 ASN A 479 0 SHEET 1 12 1 ARG A 484 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 THR B 251 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 SER 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 O2 AGLA C 1 C1 AFUC C 2 1555 1555 1.41 LINK O2 BGLA C 1 C1 BFUC C 2 1555 1555 1.39 LINK O3 AGLA C 1 C1 AGLA C 3 1555 1555 1.44 LINK O3 BGLA C 1 C1 BGLA C 3 1555 1555 1.41 LINK O2 AGLA D 1 C1 AFUC D 2 1555 1555 1.41 LINK O2 BGLA D 1 C1 BFUC D 2 1555 1555 1.42 LINK O3 AGLA D 1 C1 AGLA D 3 1555 1555 1.40 LINK O3 BGLA D 1 C1 BGLA D 3 1555 1555 1.41 CISPEP 1 GLU A 399 PRO A 400 0 -7.26 CISPEP 2 GLU B 399 PRO B 400 0 -7.71 CRYST1 113.830 58.650 97.310 90.00 107.34 90.00 C 1 2 1 8 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 0.008785 0.000000 0.002743 0.00000 SCALE2 0.000000 0.017050 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010766 0.00000