HEADER VIRAL PROTEIN 11-SEP-19 6STT TITLE ADENOVIRUS 29 FIBER KNOB PROTEIN IN COMPLEX WITH SIALIC ACID CAVEAT 6STT SIA B 401 HAS WRONG CHIRALITY AT ATOM C6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBER; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN ADENOVIRUS 29; SOURCE 3 ORGANISM_TAXID: 46931; SOURCE 4 GENE: L5; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ADENOVIRUS, TYPE 29, SIALIC ACID, 3D STRUCTURE, FIBER KNOB, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.T.BAKER,R.M.MUNDY,P.J.RIZKALLAH,A.L.PARKER REVDAT 3 11-OCT-23 6STT 1 JRNL REVDAT 2 20-SEP-23 6STT 1 JRNL REVDAT 1 31-MAR-21 6STT 0 JRNL AUTH R.M.MUNDY,A.T.BAKER,E.A.BATES,T.G.CUNLIFFE, JRNL AUTH 2 A.TEIJEIRA-CRESPO,E.MOSES,P.J.RIZKALLAH,A.L.PARKER JRNL TITL BROAD SIALIC ACID USAGE AMONGST SPECIES D HUMAN ADENOVIRUS JRNL REF NPJ VIRUSES V. 1 1 2023 JRNL DOI 10.1038/S44298-023-00001-5 REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 53165 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) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2767 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) : 1.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3880 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 206 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2852 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 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): 0.082 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.999 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2983 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2698 ; 0.004 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4064 ; 1.668 ; 1.649 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6319 ; 1.433 ; 1.576 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 358 ; 7.810 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;38.533 ;25.524 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 509 ;14.755 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;24.171 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 421 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3280 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 568 ; 0.001 ; 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): 2983 ; 4.362 ; 3.000 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 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 187 A 371 REMARK 3 ORIGIN FOR THE GROUP (A): -19.1678 -17.7965 -37.8687 REMARK 3 T TENSOR REMARK 3 T11: 0.0311 T22: 0.0078 REMARK 3 T33: 0.0761 T12: 0.0077 REMARK 3 T13: 0.0342 T23: 0.0194 REMARK 3 L TENSOR REMARK 3 L11: 2.3589 L22: 1.8114 REMARK 3 L33: 1.4527 L12: -1.0304 REMARK 3 L13: 0.4837 L23: -0.3558 REMARK 3 S TENSOR REMARK 3 S11: 0.0598 S12: 0.1245 S13: 0.2170 REMARK 3 S21: -0.1255 S22: -0.0916 S23: -0.3564 REMARK 3 S31: -0.1273 S32: 0.0162 S33: 0.0318 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 187 B 371 REMARK 3 ORIGIN FOR THE GROUP (A): -17.7830 -19.1740 -66.3991 REMARK 3 T TENSOR REMARK 3 T11: 0.0070 T22: 0.0319 REMARK 3 T33: 0.0753 T12: 0.0082 REMARK 3 T13: -0.0189 T23: -0.0352 REMARK 3 L TENSOR REMARK 3 L11: 1.8015 L22: 2.3546 REMARK 3 L33: 1.4539 L12: -1.0079 REMARK 3 L13: 0.3872 L23: -0.5223 REMARK 3 S TENSOR REMARK 3 S11: -0.0928 S12: -0.1281 S13: 0.3535 REMARK 3 S21: 0.1093 S22: 0.0656 S23: -0.2122 REMARK 3 S31: -0.0094 S32: 0.1291 S33: 0.0272 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 400 B 401 REMARK 3 ORIGIN FOR THE GROUP (A): -33.5891 -33.6237 -52.0852 REMARK 3 T TENSOR REMARK 3 T11: 0.3832 T22: 0.4573 REMARK 3 T33: 0.3029 T12: -0.0312 REMARK 3 T13: 0.0332 T23: -0.0374 REMARK 3 L TENSOR REMARK 3 L11: 0.0035 L22: 0.9426 REMARK 3 L33: 0.2323 L12: -0.0180 REMARK 3 L13: 0.0108 L23: -0.4648 REMARK 3 S TENSOR REMARK 3 S11: 0.0042 S12: -0.0354 S13: -0.0087 REMARK 3 S21: -0.2301 S22: -0.0041 S23: 0.0172 REMARK 3 S31: 0.1362 S32: -0.0265 S33: -0.0001 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 6STT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1292103395. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55982 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 60.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 22.40 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9000 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) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 22.30 REMARK 200 R MERGE FOR SHELL (I) : 2.37000 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 (%): 47.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SPG BUFFER, 25% PEG 1500, PH REMARK 280 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 3 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 350 BIOMT1 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 0.000000 0.000000 -1.000000 -104.23600 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 -104.23600 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 -104.23600 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 -104.23600 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 665 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 658 LIES ON A SPECIAL POSITION. 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 278 REMARK 465 ILE A 279 REMARK 465 LEU A 280 REMARK 465 PRO A 281 REMARK 465 GLU A 282 REMARK 465 PRO A 283 REMARK 465 TYR A 284 REMARK 465 SER B 278 REMARK 465 ILE B 279 REMARK 465 LEU B 280 REMARK 465 PRO B 281 REMARK 465 GLU B 282 REMARK 465 PRO B 283 REMARK 465 TYR B 284 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 501 O HOH B 594 1.96 REMARK 500 NZ LYS A 351 O1A SIA A 400 2.16 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 NE2 GLN A 256 O HOH B 562 3554 2.10 REMARK 500 ND2 ASN A 272 NE2 GLN B 256 4554 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 GLN A 256 C GLN A 256 O 0.254 REMARK 500 GLN B 256 C GLN B 256 O 0.255 REMARK 500 GLN B 256 C GLN B 256 O 0.265 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 ASP A 202 -66.53 -105.97 REMARK 500 CYS A 216 79.21 -119.06 REMARK 500 ASN A 325 59.62 -116.00 REMARK 500 ASN B 325 60.37 -115.67 REMARK 500 ASN B 355 41.10 71.32 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 GLN A 256 12.95 REMARK 500 GLN A 256 19.69 REMARK 500 GLN B 256 23.27 REMARK 500 GLN B 256 24.17 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 689 DISTANCE = 7.08 ANGSTROMS REMARK 525 HOH B 681 DISTANCE = 7.04 ANGSTROMS DBREF 6STT A 187 371 UNP E1CIQ3 E1CIQ3_9ADEN 187 371 DBREF 6STT B 187 371 UNP E1CIQ3 E1CIQ3_9ADEN 187 371 SEQADV 6STT LEU A 187 UNP E1CIQ3 ARG 187 CONFLICT SEQADV 6STT LEU B 187 UNP E1CIQ3 ARG 187 CONFLICT SEQRES 1 A 185 LEU THR LEU TRP THR THR LEU ASP PRO SER PRO ASN CYS SEQRES 2 A 185 LYS ILE ASP ILE GLU LYS ASP SER LYS LEU THR LEU VAL SEQRES 3 A 185 LEU THR LYS CYS GLY SER GLN ILE LEU ALA ASN VAL SER SEQRES 4 A 185 LEU ILE ILE VAL ASN GLY LYS PHE LYS ILE LEU ASN ASN SEQRES 5 A 185 LYS THR ASP PRO SER LEU PRO LYS SER PHE ASN ILE LYS SEQRES 6 A 185 LEU LEU PHE ASP GLN ASN GLY VAL LEU LEU GLU ASN SER SEQRES 7 A 185 ASN ILE GLU LYS GLN TYR LEU ASN PHE ARG SER GLY ASP SEQRES 8 A 185 SER ILE LEU PRO GLU PRO TYR LYS ASN ALA ILE GLY PHE SEQRES 9 A 185 MET PRO ASN LEU LEU ALA TYR ALA LYS ALA THR THR ASP SEQRES 10 A 185 GLN SER LYS ILE TYR ALA ARG ASN THR ILE TYR GLY ASN SEQRES 11 A 185 ILE TYR LEU ASP ASN GLN PRO TYR ASN PRO VAL VAL ILE SEQRES 12 A 185 LYS ILE THR PHE ASN ASN GLU ALA ASP SER ALA TYR SER SEQRES 13 A 185 ILE THR PHE ASN TYR SER TRP THR LYS ASP TYR ASP ASN SEQRES 14 A 185 ILE PRO PHE ASP SER THR SER PHE THR PHE SER TYR ILE SEQRES 15 A 185 ALA GLN GLU SEQRES 1 B 185 LEU THR LEU TRP THR THR LEU ASP PRO SER PRO ASN CYS SEQRES 2 B 185 LYS ILE ASP ILE GLU LYS ASP SER LYS LEU THR LEU VAL SEQRES 3 B 185 LEU THR LYS CYS GLY SER GLN ILE LEU ALA ASN VAL SER SEQRES 4 B 185 LEU ILE ILE VAL ASN GLY LYS PHE LYS ILE LEU ASN ASN SEQRES 5 B 185 LYS THR ASP PRO SER LEU PRO LYS SER PHE ASN ILE LYS SEQRES 6 B 185 LEU LEU PHE ASP GLN ASN GLY VAL LEU LEU GLU ASN SER SEQRES 7 B 185 ASN ILE GLU LYS GLN TYR LEU ASN PHE ARG SER GLY ASP SEQRES 8 B 185 SER ILE LEU PRO GLU PRO TYR LYS ASN ALA ILE GLY PHE SEQRES 9 B 185 MET PRO ASN LEU LEU ALA TYR ALA LYS ALA THR THR ASP SEQRES 10 B 185 GLN SER LYS ILE TYR ALA ARG ASN THR ILE TYR GLY ASN SEQRES 11 B 185 ILE TYR LEU ASP ASN GLN PRO TYR ASN PRO VAL VAL ILE SEQRES 12 B 185 LYS ILE THR PHE ASN ASN GLU ALA ASP SER ALA TYR SER SEQRES 13 B 185 ILE THR PHE ASN TYR SER TRP THR LYS ASP TYR ASP ASN SEQRES 14 B 185 ILE PRO PHE ASP SER THR SER PHE THR PHE SER TYR ILE SEQRES 15 B 185 ALA GLN GLU HET SIA A 400 21 HET SIA B 401 21 HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID FORMUL 3 SIA 2(C11 H19 N O9) FORMUL 5 HOH *370(H2 O) HELIX 1 AA1 GLU A 267 LEU A 271 5 5 HELIX 2 AA2 ALA A 287 MET A 291 5 5 HELIX 3 AA3 TYR A 308 ARG A 310 5 3 HELIX 4 AA4 GLU B 267 LEU B 271 5 5 HELIX 5 AA5 ALA B 287 MET B 291 5 5 HELIX 6 AA6 TYR B 308 ARG B 310 5 3 SHEET 1 AA1 5 ASN A 272 PHE A 273 0 SHEET 2 AA1 5 THR A 188 TRP A 190 -1 N TRP A 190 O ASN A 272 SHEET 3 AA1 5 SER A 207 CYS A 216 -1 O LEU A 213 N LEU A 189 SHEET 4 AA1 5 GLN A 219 ILE A 228 -1 O LEU A 221 N THR A 214 SHEET 5 AA1 5 PHE A 363 ILE A 368 -1 O PHE A 365 N ALA A 222 SHEET 1 AA2 2 ILE A 235 LEU A 236 0 SHEET 2 AA2 2 ILE A 356 PRO A 357 -1 O ILE A 356 N LEU A 236 SHEET 1 AA3 4 SER A 247 PHE A 254 0 SHEET 2 AA3 4 TYR A 341 SER A 348 -1 O TYR A 341 N PHE A 254 SHEET 3 AA3 4 PRO A 326 PHE A 333 -1 N LYS A 330 O ASN A 346 SHEET 4 AA3 4 THR A 312 TYR A 318 -1 N ILE A 313 O ILE A 331 SHEET 1 AA4 5 ASN B 272 PHE B 273 0 SHEET 2 AA4 5 THR B 188 TRP B 190 -1 N TRP B 190 O ASN B 272 SHEET 3 AA4 5 SER B 207 CYS B 216 -1 O LEU B 213 N LEU B 189 SHEET 4 AA4 5 GLN B 219 ILE B 228 -1 O GLN B 219 N CYS B 216 SHEET 5 AA4 5 PHE B 363 ILE B 368 -1 O PHE B 365 N ALA B 222 SHEET 1 AA5 2 ILE B 235 LEU B 236 0 SHEET 2 AA5 2 ILE B 356 PRO B 357 -1 O ILE B 356 N LEU B 236 SHEET 1 AA6 4 SER B 247 PHE B 254 0 SHEET 2 AA6 4 TYR B 341 SER B 348 -1 O TYR B 341 N PHE B 254 SHEET 3 AA6 4 PRO B 326 PHE B 333 -1 N LYS B 330 O ASN B 346 SHEET 4 AA6 4 THR B 312 TYR B 318 -1 N ILE B 313 O ILE B 331 CRYST1 104.236 104.236 104.236 90.00 90.00 90.00 P 2 3 24 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 0.009594 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009594 0.00000