HEADER VIRAL PROTEIN 10-JAN-19 6QFY TITLE CRYSTAL STRUCTURE OF PORCINE HEMAGGLUTINATING ENCEPHALOMYELITIS VIRUS TITLE 2 SPIKE PROTEIN LECTIN DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORCINE HEMAGGLUTINATING ENCEPHALOMYELITIS SOURCE 3 VIRUS; SOURCE 4 ORGANISM_TAXID: 42005; SOURCE 5 VARIANT: UU; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293-GNTI(-); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCAGGS-TX-FC KEYWDS SIALIC ACID BINDING, BETA-SANDWICH, VIRAL SPIKE PROTEIN, SPIKE-NTD, KEYWDS 2 VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.G.HUIZINGA,M.BAKKERS,Y.LANG REVDAT 4 24-JAN-24 6QFY 1 HETSYN REVDAT 3 29-JUL-20 6QFY 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 20-FEB-19 6QFY 1 JRNL REVDAT 1 06-FEB-19 6QFY 0 JRNL AUTH R.J.G.HULSWIT,Y.LANG,M.J.G.BAKKERS,W.LI,Z.LI,A.SCHOUTEN, JRNL AUTH 2 B.OPHORST,F.J.M.VAN KUPPEVELD,G.J.BOONS,B.J.BOSCH, JRNL AUTH 3 E.G.HUIZINGA,R.J.DE GROOT JRNL TITL HUMAN CORONAVIRUSES OC43 AND HKU1 BIND TO 9-O-ACETYLATED JRNL TITL 2 SIALIC ACIDS VIA A CONSERVED RECEPTOR-BINDING SITE IN SPIKE JRNL TITL 3 PROTEIN DOMAIN A. JRNL REF PROC. NATL. ACAD. SCI. V. 116 2681 2019 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 30679277 JRNL DOI 10.1073/PNAS.1809667116 REMARK 2 REMARK 2 RESOLUTION. 2.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0232 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 19442 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 985 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1171 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.4160 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.4690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4538 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 193 REMARK 3 SOLVENT ATOMS : 30 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 94.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 93.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.17000 REMARK 3 B22 (A**2) : 1.17000 REMARK 3 B33 (A**2) : -3.80000 REMARK 3 B12 (A**2) : 0.59000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 2.330 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.390 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.404 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 55.542 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4882 ; 0.005 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4260 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6689 ; 1.383 ; 1.700 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9887 ; 1.110 ; 1.618 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 570 ; 8.299 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 222 ;31.077 ;22.793 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 702 ;14.452 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;18.527 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 678 ; 0.044 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5356 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1084 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 15 297 B 15 297 8788 0.060 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 302 REMARK 3 ORIGIN FOR THE GROUP (A): -6.2670 74.1961 34.3872 REMARK 3 T TENSOR REMARK 3 T11: 0.4714 T22: 0.3778 REMARK 3 T33: 0.0170 T12: -0.0169 REMARK 3 T13: -0.0243 T23: -0.0287 REMARK 3 L TENSOR REMARK 3 L11: 2.4949 L22: 2.1346 REMARK 3 L33: 3.1287 L12: -0.2090 REMARK 3 L13: -0.9662 L23: -0.2597 REMARK 3 S TENSOR REMARK 3 S11: -0.0805 S12: -0.0083 S13: -0.1747 REMARK 3 S21: 0.1304 S22: 0.0161 S23: 0.0351 REMARK 3 S31: -0.0142 S32: 0.0235 S33: 0.0644 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 298 REMARK 3 ORIGIN FOR THE GROUP (A): -20.8685 90.1305 2.2618 REMARK 3 T TENSOR REMARK 3 T11: 0.4589 T22: 0.5679 REMARK 3 T33: 0.0828 T12: 0.0687 REMARK 3 T13: -0.0221 T23: 0.0308 REMARK 3 L TENSOR REMARK 3 L11: 1.9076 L22: 3.3560 REMARK 3 L33: 3.4208 L12: -0.3259 REMARK 3 L13: -1.0007 L23: 0.6489 REMARK 3 S TENSOR REMARK 3 S11: 0.1786 S12: 0.2795 S13: 0.0412 REMARK 3 S21: -0.1390 S22: -0.1742 S23: 0.4963 REMARK 3 S31: -0.4363 S32: -0.3247 S33: -0.0044 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6QFY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1292100086. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9677 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20445 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.970 REMARK 200 RESOLUTION RANGE LOW (A) : 97.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.15400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 1.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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: 4H14 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM MGCL2, 100 MM BISTRIS 5.5, 25% REMARK 280 (W/V) PEG3350, PH 5.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.14700 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 94.29400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 94.29400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.14700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, F, G 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 B 299 REMARK 465 SER B 300 REMARK 465 ASP B 301 REMARK 465 PRO B 302 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 LYS A 20 CG CD CE NZ REMARK 470 ASP A 54 CG OD1 OD2 REMARK 470 MET A 295 CG SD CE REMARK 470 LYS B 20 CG CD CE NZ REMARK 470 ASP B 54 CG OD1 OD2 REMARK 470 LYS B 231 CG CD CE NZ REMARK 470 SER B 292 OG REMARK 470 GLU B 293 CG CD OE1 OE2 REMARK 470 MET B 295 CG SD CE 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 A 610 O HOH A 615 2.02 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 OD2 ASP A 289 OH TYR B 281 6655 1.82 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 22 O - C - N ANGL. DEV. = 16.6 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 ILE A 16 -70.13 -105.90 REMARK 500 ASP A 18 52.91 -150.38 REMARK 500 CYS A 21 -141.41 -82.09 REMARK 500 ASN A 22 76.10 -69.12 REMARK 500 ASN A 45 54.88 -150.18 REMARK 500 LEU A 62 103.92 -164.95 REMARK 500 THR A 83 -65.71 -123.81 REMARK 500 ASN A 100 -115.75 -99.50 REMARK 500 SER A 120 79.39 -155.57 REMARK 500 SER A 129 -83.72 -96.98 REMARK 500 LEU A 183 102.85 -162.41 REMARK 500 ASP A 187 54.84 -141.99 REMARK 500 TYR A 195 138.93 -170.21 REMARK 500 LEU A 233 -67.10 -104.61 REMARK 500 ASP A 275 176.22 -55.96 REMARK 500 THR A 298 75.70 -61.31 REMARK 500 SER A 299 78.64 -157.70 REMARK 500 SER A 300 39.97 -175.51 REMARK 500 ASP A 301 65.20 87.65 REMARK 500 ILE B 16 -70.95 -106.29 REMARK 500 ASP B 18 52.71 -151.10 REMARK 500 CYS B 21 -137.28 -81.61 REMARK 500 ASN B 22 78.82 -66.88 REMARK 500 ASN B 45 53.63 -150.15 REMARK 500 LEU B 62 103.69 -165.13 REMARK 500 THR B 83 -67.72 -123.54 REMARK 500 ASN B 100 -117.36 -101.28 REMARK 500 SER B 120 80.06 -154.35 REMARK 500 SER B 129 -83.24 -96.09 REMARK 500 LEU B 183 103.08 -162.08 REMARK 500 LEU B 233 -64.71 -104.35 REMARK 500 ASP B 275 175.93 -55.90 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6QFY A 15 300 UNP A0A1Z2WUW0_9BETC DBREF2 6QFY A A0A1Z2WUW0 15 300 DBREF1 6QFY B 15 300 UNP A0A1Z2WUW0_9BETC DBREF2 6QFY B A0A1Z2WUW0 15 300 SEQADV 6QFY ASP A 301 UNP A0A1Z2WUW EXPRESSION TAG SEQADV 6QFY PRO A 302 UNP A0A1Z2WUW EXPRESSION TAG SEQADV 6QFY ASP B 301 UNP A0A1Z2WUW EXPRESSION TAG SEQADV 6QFY PRO B 302 UNP A0A1Z2WUW EXPRESSION TAG SEQRES 1 A 288 VAL ILE GLY ASP LEU LYS CYS ASN THR SER SER ILE ASN SEQRES 2 A 288 ASP VAL ASP THR GLY VAL PRO SER ILE SER SER GLU VAL SEQRES 3 A 288 VAL ASP VAL THR ASN GLY LEU GLY THR PHE TYR VAL LEU SEQRES 4 A 288 ASP ARG VAL TYR LEU ASN THR THR LEU LEU LEU ASN GLY SEQRES 5 A 288 TYR TYR PRO ILE SER GLY ALA THR PHE ARG ASN MET ALA SEQRES 6 A 288 LEU LYS GLY THR ARG LEU LEU SER THR LEU TRP PHE LYS SEQRES 7 A 288 SER PRO PHE LEU SER PRO PHE ASN ASP GLY ILE PHE ALA SEQRES 8 A 288 LYS VAL LYS ASN SER ARG PHE SER LYS ASP GLY VAL ILE SEQRES 9 A 288 TYR SER GLU PHE PRO ALA ILE THR ILE GLY SER THR PHE SEQRES 10 A 288 VAL ASN SER SER HIS SER ILE VAL VAL LYS PRO HIS THR SEQRES 11 A 288 SER PHE ILE ASN GLY ASN LEU GLN GLY LEU LEU GLN ILE SEQRES 12 A 288 SER VAL CYS GLN TYR THR MET CYS GLU TYR PRO HIS THR SEQRES 13 A 288 ILE CYS HIS PRO ASN LEU GLY ASN GLN ARG ILE GLU LEU SEQRES 14 A 288 TRP HIS TYR ASP THR ASP VAL VAL SER CYS LEU TYR LYS SEQRES 15 A 288 ARG ASN PHE THR TYR ASP VAL ASN ALA ASP TYR LEU TYR SEQRES 16 A 288 PHE HIS PHE TYR GLN GLU GLY GLY THR PHE TYR ALA TYR SEQRES 17 A 288 PHE THR ASP THR GLY PHE VAL THR LYS PHE LEU PHE LYS SEQRES 18 A 288 LEU TYR LEU GLY THR VAL LEU SER HIS TYR TYR VAL MET SEQRES 19 A 288 PRO LEU THR CYS ASP SER ALA LEU SER LEU GLU TYR TRP SEQRES 20 A 288 VAL THR PRO LEU THR THR ARG GLN PHE LEU LEU ALA PHE SEQRES 21 A 288 ASP GLN ASP GLY VAL LEU TYR HIS ALA VAL ASP CYS ALA SEQRES 22 A 288 SER ASP PHE MET SER GLU ILE MET CYS LYS THR SER SER SEQRES 23 A 288 ASP PRO SEQRES 1 B 288 VAL ILE GLY ASP LEU LYS CYS ASN THR SER SER ILE ASN SEQRES 2 B 288 ASP VAL ASP THR GLY VAL PRO SER ILE SER SER GLU VAL SEQRES 3 B 288 VAL ASP VAL THR ASN GLY LEU GLY THR PHE TYR VAL LEU SEQRES 4 B 288 ASP ARG VAL TYR LEU ASN THR THR LEU LEU LEU ASN GLY SEQRES 5 B 288 TYR TYR PRO ILE SER GLY ALA THR PHE ARG ASN MET ALA SEQRES 6 B 288 LEU LYS GLY THR ARG LEU LEU SER THR LEU TRP PHE LYS SEQRES 7 B 288 SER PRO PHE LEU SER PRO PHE ASN ASP GLY ILE PHE ALA SEQRES 8 B 288 LYS VAL LYS ASN SER ARG PHE SER LYS ASP GLY VAL ILE SEQRES 9 B 288 TYR SER GLU PHE PRO ALA ILE THR ILE GLY SER THR PHE SEQRES 10 B 288 VAL ASN SER SER HIS SER ILE VAL VAL LYS PRO HIS THR SEQRES 11 B 288 SER PHE ILE ASN GLY ASN LEU GLN GLY LEU LEU GLN ILE SEQRES 12 B 288 SER VAL CYS GLN TYR THR MET CYS GLU TYR PRO HIS THR SEQRES 13 B 288 ILE CYS HIS PRO ASN LEU GLY ASN GLN ARG ILE GLU LEU SEQRES 14 B 288 TRP HIS TYR ASP THR ASP VAL VAL SER CYS LEU TYR LYS SEQRES 15 B 288 ARG ASN PHE THR TYR ASP VAL ASN ALA ASP TYR LEU TYR SEQRES 16 B 288 PHE HIS PHE TYR GLN GLU GLY GLY THR PHE TYR ALA TYR SEQRES 17 B 288 PHE THR ASP THR GLY PHE VAL THR LYS PHE LEU PHE LYS SEQRES 18 B 288 LEU TYR LEU GLY THR VAL LEU SER HIS TYR TYR VAL MET SEQRES 19 B 288 PRO LEU THR CYS ASP SER ALA LEU SER LEU GLU TYR TRP SEQRES 20 B 288 VAL THR PRO LEU THR THR ARG GLN PHE LEU LEU ALA PHE SEQRES 21 B 288 ASP GLN ASP GLY VAL LEU TYR HIS ALA VAL ASP CYS ALA SEQRES 22 B 288 SER ASP PHE MET SER GLU ILE MET CYS LYS THR SER SER SEQRES 23 B 288 ASP PRO HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET NAG F 1 14 HET NAG F 2 14 HET NAG G 1 14 HET NAG G 2 14 HET NAG A 501 14 HET NAG A 506 14 HET NAG B 504 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE 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 BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 3 NAG 13(C8 H15 N O6) FORMUL 5 BMA C6 H12 O6 FORMUL 11 HOH *30(H2 O) HELIX 1 AA1 LEU A 89 LYS A 92 5 4 HELIX 2 AA2 HIS A 173 GLY A 177 5 5 HELIX 3 AA3 ASP A 289 THR A 298 1 10 HELIX 4 AA4 LEU B 89 LYS B 92 5 4 HELIX 5 AA5 HIS B 173 GLY B 177 5 5 HELIX 6 AA6 ASP B 289 CYS B 296 1 8 SHEET 1 AA1 2 ILE A 26 ASN A 27 0 SHEET 2 AA1 2 LEU A 86 SER A 87 1 O LEU A 86 N ASN A 27 SHEET 1 AA2 7 SER A 35 VAL A 40 0 SHEET 2 AA2 7 THR A 74 ASN A 77 -1 O ASN A 77 N SER A 35 SHEET 3 AA2 7 TYR A 260 PHE A 274 -1 O VAL A 262 N ARG A 76 SHEET 4 AA2 7 GLY A 102 LYS A 108 -1 N PHE A 104 O THR A 263 SHEET 5 AA2 7 TYR A 207 GLU A 215 -1 O LEU A 208 N VAL A 107 SHEET 6 AA2 7 THR A 218 THR A 224 -1 O TYR A 220 N TYR A 213 SHEET 7 AA2 7 LYS A 231 TYR A 237 -1 O LEU A 236 N PHE A 219 SHEET 1 AA3 3 THR A 60 PRO A 69 0 SHEET 2 AA3 3 TYR A 260 PHE A 274 -1 O PHE A 270 N LEU A 64 SHEET 3 AA3 3 LEU A 280 ASP A 285 -1 O VAL A 284 N LEU A 271 SHEET 1 AA4 4 LYS A 81 GLY A 82 0 SHEET 2 AA4 4 LEU A 250 THR A 251 1 O LEU A 250 N GLY A 82 SHEET 3 AA4 4 MET A 164 ILE A 171 1 N THR A 170 O THR A 251 SHEET 4 AA4 4 LEU A 183 HIS A 185 -1 O TRP A 184 N CYS A 165 SHEET 1 AA5 6 SER A 97 PRO A 98 0 SHEET 2 AA5 6 HIS A 244 VAL A 247 -1 O TYR A 245 N SER A 97 SHEET 3 AA5 6 ILE A 125 GLY A 128 -1 N THR A 126 O TYR A 246 SHEET 4 AA5 6 SER A 137 ILE A 147 -1 O ILE A 138 N ILE A 127 SHEET 5 AA5 6 ASN A 150 CYS A 160 -1 O GLN A 152 N SER A 145 SHEET 6 AA5 6 CYS A 193 ARG A 197 -1 O TYR A 195 N VAL A 159 SHEET 1 AA6 2 SER A 113 LYS A 114 0 SHEET 2 AA6 2 VAL A 117 ILE A 118 -1 O VAL A 117 N LYS A 114 SHEET 1 AA7 2 ILE B 26 ASN B 27 0 SHEET 2 AA7 2 LEU B 86 SER B 87 1 O LEU B 86 N ASN B 27 SHEET 1 AA8 7 SER B 35 VAL B 40 0 SHEET 2 AA8 7 THR B 74 ASN B 77 -1 O ASN B 77 N SER B 35 SHEET 3 AA8 7 TYR B 260 PHE B 274 -1 O VAL B 262 N ARG B 76 SHEET 4 AA8 7 GLY B 102 LYS B 108 -1 N PHE B 104 O THR B 263 SHEET 5 AA8 7 TYR B 207 GLU B 215 -1 O LEU B 208 N VAL B 107 SHEET 6 AA8 7 THR B 218 THR B 224 -1 O TYR B 220 N TYR B 213 SHEET 7 AA8 7 LYS B 231 TYR B 237 -1 O LEU B 236 N PHE B 219 SHEET 1 AA9 3 THR B 60 PRO B 69 0 SHEET 2 AA9 3 TYR B 260 PHE B 274 -1 O PHE B 270 N LEU B 64 SHEET 3 AA9 3 LEU B 280 ASP B 285 -1 O VAL B 284 N LEU B 271 SHEET 1 AB1 4 LYS B 81 GLY B 82 0 SHEET 2 AB1 4 LEU B 250 THR B 251 1 O LEU B 250 N GLY B 82 SHEET 3 AB1 4 MET B 164 ILE B 171 1 N THR B 170 O THR B 251 SHEET 4 AB1 4 LEU B 183 HIS B 185 -1 O TRP B 184 N CYS B 165 SHEET 1 AB2 6 SER B 97 PRO B 98 0 SHEET 2 AB2 6 HIS B 244 VAL B 247 -1 O TYR B 245 N SER B 97 SHEET 3 AB2 6 ILE B 125 GLY B 128 -1 N THR B 126 O TYR B 246 SHEET 4 AB2 6 SER B 137 ILE B 147 -1 O ILE B 138 N ILE B 127 SHEET 5 AB2 6 ASN B 150 CYS B 160 -1 O GLN B 152 N SER B 145 SHEET 6 AB2 6 CYS B 193 ARG B 197 -1 O TYR B 195 N VAL B 159 SHEET 1 AB3 2 SER B 113 LYS B 114 0 SHEET 2 AB3 2 VAL B 117 ILE B 118 -1 O VAL B 117 N LYS B 114 SSBOND 1 CYS A 21 CYS A 165 1555 1555 2.06 SSBOND 2 CYS A 160 CYS A 193 1555 1555 2.06 SSBOND 3 CYS A 172 CYS A 252 1555 1555 2.06 SSBOND 4 CYS A 286 CYS A 296 1555 1555 2.02 SSBOND 5 CYS B 21 CYS B 165 1555 1555 2.07 SSBOND 6 CYS B 160 CYS B 193 1555 1555 2.06 SSBOND 7 CYS B 172 CYS B 252 1555 1555 2.06 SSBOND 8 CYS B 286 CYS B 296 1555 1555 2.05 LINK ND2 ASN A 22 C1 NAG A 501 1555 1555 1.45 LINK ND2 ASN A 59 C1 NAG A 506 1555 1555 1.44 LINK ND2 ASN A 133 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN A 198 C1 NAG D 1 1555 1555 1.44 LINK ND2 ASN B 22 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN B 59 C1 NAG B 504 1555 1555 1.45 LINK ND2 ASN B 133 C1 NAG F 1 1555 1555 1.45 LINK ND2 ASN B 198 C1 NAG G 1 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.45 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.45 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.45 LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.44 CISPEP 1 SER A 93 PRO A 94 0 13.00 CISPEP 2 SER B 93 PRO B 94 0 13.87 CRYST1 112.572 112.572 141.441 90.00 90.00 120.00 P 31 2 1 12 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 0.008883 0.005129 0.000000 0.00000 SCALE2 0.000000 0.010257 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007070 0.00000