PDB Short entry for 3GVJ HEADER HYDROLASE 31-MAR-09 3GVJ TITLE CRYSTAL STRUCTURE OF AN ENDO-NEURAMINIDASENF MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-N-ACETYLNEURAMINIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 246-910; COMPND 5 SYNONYM: ENDO-ALPHA-SIALIDASE, GP17 PROTEIN; COMPND 6 EC: 3.2.1.129; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE K1F; SOURCE 3 ORGANISM_COMMON: BACTERIOPHAGE K1F; SOURCE 4 ORGANISM_TAXID: 344021; SOURCE 5 GENE: SIA, 17, 17.0; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENDO-NEURAMINIDASE; POLYSIALIC ACID; TRIPLE-BETA HELIX, GLYCOSIDASE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.C.SCHULZ,A.DICKMANNS,R.FICNER REVDAT 6 21-FEB-24 3GVJ 1 REMARK REVDAT 5 13-OCT-21 3GVJ 1 SEQADV HETSYN REVDAT 4 29-JUL-20 3GVJ 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 13-JUL-11 3GVJ 1 VERSN REVDAT 2 28-APR-10 3GVJ 1 JRNL REVDAT 1 02-MAR-10 3GVJ 0 JRNL AUTH E.C.SCHULZ,D.SCHWARZER,M.FRANK,K.STUMMEYER,M.MUHLENHOFF, JRNL AUTH 2 A.DICKMANNS,R.GERARDY-SCHAHN,R.FICNER JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION AND CLEAVAGE OF JRNL TITL 2 POLYSIALIC ACID BY THE BACTERIOPHAGE K1F TAILSPIKE PROTEIN JRNL TITL 3 ENDONF. JRNL REF J.MOL.BIOL. V. 397 341 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20096705 JRNL DOI 10.1016/J.JMB.2010.01.028 REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0039 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 147036 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7739 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) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10697 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 564 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5253 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 182 REMARK 3 SOLVENT ATOMS : 850 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.24000 REMARK 3 B22 (A**2) : 0.24000 REMARK 3 B33 (A**2) : -0.37000 REMARK 3 B12 (A**2) : 0.12000 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): 0.067 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.524 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5787 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7925 ; 1.471 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 723 ; 7.095 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 281 ;33.346 ;23.488 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 853 ;11.887 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 43 ;13.912 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 866 ; 0.131 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4567 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3431 ; 0.515 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5587 ; 0.880 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2356 ; 1.505 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2319 ; 2.228 ; 4.500 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 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 245 A 275 REMARK 3 ORIGIN FOR THE GROUP (A): 50.3220 47.5632 33.1273 REMARK 3 T TENSOR REMARK 3 T11: 0.0038 T22: 0.0287 REMARK 3 T33: 0.0096 T12: 0.0001 REMARK 3 T13: -0.0009 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 1.7031 L22: 1.0908 REMARK 3 L33: 0.6063 L12: -0.2032 REMARK 3 L13: -0.1706 L23: -0.0238 REMARK 3 S TENSOR REMARK 3 S11: 0.0049 S12: -0.2146 S13: 0.0920 REMARK 3 S21: 0.0381 S22: 0.0018 S23: -0.0764 REMARK 3 S31: 0.0076 S32: 0.0233 S33: -0.0067 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 : A 777 A 910 REMARK 3 ORIGIN FOR THE GROUP (A): 61.5597 35.8090 -44.5517 REMARK 3 T TENSOR REMARK 3 T11: 0.0045 T22: 0.0025 REMARK 3 T33: 0.0027 T12: -0.0011 REMARK 3 T13: 0.0010 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.1403 L22: 0.1475 REMARK 3 L33: 0.4466 L12: -0.0308 REMARK 3 L13: 0.0242 L23: -0.0483 REMARK 3 S TENSOR REMARK 3 S11: -0.0046 S12: 0.0187 S13: 0.0171 REMARK 3 S21: -0.0225 S22: -0.0019 S23: -0.0132 REMARK 3 S31: -0.0078 S32: 0.0046 S33: 0.0064 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 423 A 511 REMARK 3 ORIGIN FOR THE GROUP (A): 34.4063 3.4790 -12.3910 REMARK 3 T TENSOR REMARK 3 T11: 0.0241 T22: 0.0099 REMARK 3 T33: 0.0473 T12: 0.0007 REMARK 3 T13: -0.0335 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.8052 L22: 0.5553 REMARK 3 L33: 0.4579 L12: 0.1200 REMARK 3 L13: 0.5034 L23: 0.1069 REMARK 3 S TENSOR REMARK 3 S11: 0.0732 S12: 0.0084 S13: -0.1108 REMARK 3 S21: 0.0280 S22: -0.0023 S23: -0.0300 REMARK 3 S31: 0.0405 S32: -0.0319 S33: -0.0709 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK 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: U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 3GVJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000052359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 164778 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 46.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 8000, 0.1M TRIS/HCL, PH REMARK 280 7.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 59.54500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.37832 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 58.66000 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 59.54500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 34.37832 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.66000 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 59.54500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 34.37832 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.66000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 68.75664 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 117.32000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 68.75664 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 117.32000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 68.75664 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 117.32000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 51920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 67290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -145.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 119.09000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 59.54500 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 103.13497 REMARK 350 BIOMT3 3 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 A1096 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1420 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1485 LIES ON A SPECIAL POSITION. 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 O8 SLB B 1 O6 SIA B 2 2.19 REMARK 500 O8 SLB C 1 O6 SIA C 2 2.19 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 TYR A 296 CD1 TYR A 296 CE1 -0.090 REMARK 500 GLU A 297 CD GLU A 297 OE2 -0.067 REMARK 500 TYR A 344 CE1 TYR A 344 CZ -0.081 REMARK 500 TYR A 344 CE2 TYR A 344 CD2 -0.097 REMARK 500 GLU A 373 CD GLU A 373 OE1 -0.080 REMARK 500 GLY A 504 C THR A 505 N 0.149 REMARK 500 GLY A 504 C THR A 505 N 0.158 REMARK 500 GLU A 574 N GLU A 574 CA -0.131 REMARK 500 GLU A 576 CD GLU A 576 OE2 -0.068 REMARK 500 TYR A 661 CZ TYR A 661 CE2 -0.088 REMARK 500 GLY A 851 C GLY A 851 O -0.096 REMARK 500 GLU A 873 CD GLU A 873 OE2 -0.071 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 MET A 503 CA - C - N ANGL. DEV. = 30.1 DEGREES REMARK 500 MET A 503 CA - C - N ANGL. DEV. = 30.5 DEGREES REMARK 500 MET A 503 O - C - N ANGL. DEV. = -28.3 DEGREES REMARK 500 MET A 503 O - C - N ANGL. DEV. = -28.7 DEGREES REMARK 500 LEU A 620 CA - CB - CG ANGL. DEV. = 17.8 DEGREES REMARK 500 ARG A 865 NE - CZ - NH2 ANGL. DEV. = -5.7 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 VAL A 251 -42.25 -131.78 REMARK 500 VAL A 251 -56.50 -122.64 REMARK 500 ASP A 285 85.72 -69.11 REMARK 500 GLU A 310 -3.95 75.63 REMARK 500 ASP A 321 76.75 -153.01 REMARK 500 ASN A 338 -2.35 73.02 REMARK 500 SER A 347 -156.49 -133.05 REMARK 500 ARG A 354 15.81 58.19 REMARK 500 ARG A 396 59.48 39.93 REMARK 500 SER A 528 163.23 80.37 REMARK 500 ASP A 533 -157.11 -156.50 REMARK 500 HIS A 624 34.18 73.82 REMARK 500 HIS A 628 -6.18 73.02 REMARK 500 TYR A 665 79.05 -118.57 REMARK 500 VAL A 704 68.82 33.05 REMARK 500 ASP A 711 -127.32 53.61 REMARK 500 SER A 740 -130.47 50.84 REMARK 500 SER A 806 -21.62 -147.23 REMARK 500 SER A 808 68.45 63.35 REMARK 500 SER A 878 -7.32 75.24 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 ARG A 243 GLY A 244 39.08 REMARK 500 GLN A 330 ASP A 331 -30.68 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 MET A 503 -13.51 REMARK 500 MET A 503 -13.63 REMARK 500 REMARK 500 REMARK: NULL DBREF 3GVJ A 246 910 UNP Q858B1 Q858B1_BPK1F 246 910 SEQADV 3GVJ VAL A 241 UNP Q858B1 EXPRESSION TAG SEQADV 3GVJ PRO A 242 UNP Q858B1 EXPRESSION TAG SEQADV 3GVJ ARG A 243 UNP Q858B1 EXPRESSION TAG SEQADV 3GVJ GLY A 244 UNP Q858B1 EXPRESSION TAG SEQADV 3GVJ SER A 245 UNP Q858B1 EXPRESSION TAG SEQADV 3GVJ ALA A 647 UNP Q858B1 ARG 647 ENGINEERED MUTATION SEQRES 1 A 670 VAL PRO ARG GLY SER ALA LYS GLY ASP GLY VAL THR ASP SEQRES 2 A 670 ASP THR ALA ALA LEU THR SER ALA LEU ASN ASP THR PRO SEQRES 3 A 670 VAL GLY GLN LYS ILE ASN GLY ASN GLY LYS THR TYR LYS SEQRES 4 A 670 VAL THR SER LEU PRO ASP ILE SER ARG PHE ILE ASN THR SEQRES 5 A 670 ARG PHE VAL TYR GLU ARG ILE PRO GLY GLN PRO LEU TYR SEQRES 6 A 670 TYR ALA SER GLU GLU PHE VAL GLN GLY GLU LEU PHE LYS SEQRES 7 A 670 ILE THR ASP THR PRO TYR TYR ASN ALA TRP PRO GLN ASP SEQRES 8 A 670 LYS ALA PHE VAL TYR GLU ASN VAL ILE TYR ALA PRO TYR SEQRES 9 A 670 MET GLY SER ASP ARG HIS GLY VAL SER ARG LEU HIS VAL SEQRES 10 A 670 SER TRP VAL LYS SER GLY ASP ASP GLY GLN THR TRP SER SEQRES 11 A 670 THR PRO GLU TRP LEU THR ASP LEU HIS PRO ASP TYR PRO SEQRES 12 A 670 THR VAL ASN TYR HIS CYS MET SER MET GLY VAL CYS ARG SEQRES 13 A 670 ASN ARG LEU PHE ALA MET ILE GLU THR ARG THR LEU ALA SEQRES 14 A 670 LYS ASN ALA LEU THR ASN CYS ALA LEU TRP ASP ARG PRO SEQRES 15 A 670 MET SER ARG SER LEU HIS LEU THR GLY GLY ILE THR LYS SEQRES 16 A 670 ALA ALA ASN GLN ARG TYR ALA THR ILE HIS VAL PRO ASP SEQRES 17 A 670 HIS GLY LEU PHE VAL GLY ASP PHE VAL ASN PHE SER ASN SEQRES 18 A 670 SER ALA VAL THR GLY VAL SER GLY ASP MET THR VAL ALA SEQRES 19 A 670 THR VAL ILE ASP LYS ASP ASN PHE THR VAL LEU THR PRO SEQRES 20 A 670 ASN GLN GLN THR SER ASP LEU ASN ASN ALA GLY LYS ASN SEQRES 21 A 670 TRP HIS MET GLY THR SER PHE HIS LYS SER PRO TRP ARG SEQRES 22 A 670 LYS THR ASP LEU GLY LEU ILE PRO SER VAL THR GLU VAL SEQRES 23 A 670 HIS SER PHE ALA THR ILE ASP ASN ASN GLY PHE ALA MET SEQRES 24 A 670 GLY TYR HIS GLN GLY ASP VAL ALA PRO ARG GLU VAL GLY SEQRES 25 A 670 LEU PHE TYR PHE PRO ASP ALA PHE ASN SER PRO SER ASN SEQRES 26 A 670 TYR VAL ARG ARG GLN ILE PRO SER GLU TYR GLU PRO ASP SEQRES 27 A 670 ALA SER GLU PRO CYS ILE LYS TYR TYR ASP GLY VAL LEU SEQRES 28 A 670 TYR LEU ILE THR ARG GLY THR ARG GLY ASP ARG LEU GLY SEQRES 29 A 670 SER SER LEU HIS ARG SER ARG ASP ILE GLY GLN THR TRP SEQRES 30 A 670 GLU SER LEU ARG PHE PRO HIS ASN VAL HIS HIS THR THR SEQRES 31 A 670 LEU PRO PHE ALA LYS VAL GLY ASP ASP LEU ILE MET PHE SEQRES 32 A 670 GLY SER GLU ALA ALA GLU ASN GLU TRP GLU ALA GLY ALA SEQRES 33 A 670 PRO ASP ASP ARG TYR LYS ALA SER TYR PRO ARG THR PHE SEQRES 34 A 670 TYR ALA ARG LEU ASN VAL ASN ASN TRP ASN ALA ASP ASP SEQRES 35 A 670 ILE GLU TRP VAL ASN ILE THR ASP GLN ILE TYR GLN GLY SEQRES 36 A 670 GLY ILE VAL ASN SER GLY VAL GLY VAL GLY SER VAL VAL SEQRES 37 A 670 VAL LYS ASP ASN TYR ILE TYR TYR MET PHE GLY GLY GLU SEQRES 38 A 670 ASP HIS PHE ASN PRO TRP THR TYR GLY ASP ASN SER ALA SEQRES 39 A 670 LYS ASP PRO PHE LYS SER ASP GLY HIS PRO SER ASP LEU SEQRES 40 A 670 TYR CYS TYR LYS MET LYS ILE GLY PRO ASP ASN ARG VAL SEQRES 41 A 670 SER ARG ASP PHE ARG TYR GLY ALA VAL PRO ASN ARG ALA SEQRES 42 A 670 VAL PRO VAL PHE PHE ASP THR ASN GLY VAL ARG THR VAL SEQRES 43 A 670 PRO ALA PRO MET GLU PHE THR GLY ASP LEU GLY LEU GLY SEQRES 44 A 670 HIS VAL THR ILE ARG ALA SER THR SER SER ASN ILE ARG SEQRES 45 A 670 SER GLU VAL LEU MET GLU GLY GLU TYR GLY PHE ILE GLY SEQRES 46 A 670 LYS SER ILE PRO THR ASP ASN PRO ALA GLY GLN ARG ILE SEQRES 47 A 670 ILE PHE CYS GLY GLY GLU GLY THR SER SER THR THR GLY SEQRES 48 A 670 ALA GLN ILE THR LEU TYR GLY ALA ASN ASN THR ASP SER SEQRES 49 A 670 ARG ARG ILE VAL TYR ASN GLY ASP GLU HIS LEU PHE GLN SEQRES 50 A 670 SER ALA ASP VAL LYS PRO TYR ASN ASP ASN VAL THR ALA SEQRES 51 A 670 LEU GLY GLY PRO SER ASN ARG PHE THR THR ALA TYR LEU SEQRES 52 A 670 GLY SER ASN PRO ILE VAL THR HET SLB B 1 21 HET SIA B 2 20 HET SIA B 3 20 HET SIA B 4 20 HET SIA B 5 20 HET SLB C 1 21 HET SIA C 2 20 HET SIA C 3 20 HET SIA C 4 20 HETNAM SLB N-ACETYL-BETA-NEURAMINIC ACID HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID HETSYN SLB N-ACETYLNEURAMINIC ACID; SIALIC ACID; O-SIALIC ACID; 5- HETSYN 2 SLB N-ACETYL-BETA-D-NEURAMINIC ACID; BETA-SIALIC ACID HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID FORMUL 2 SLB 2(C11 H19 N O9) FORMUL 2 SIA 7(C11 H19 N O9) FORMUL 4 HOH *850(H2 O) HELIX 1 1 ASP A 254 THR A 265 1 12 HELIX 2 2 ASP A 285 SER A 287 5 3 HELIX 3 3 PRO A 572 GLU A 576 5 5 HELIX 4 4 ASN A 832 GLY A 835 5 4 HELIX 5 5 SER A 847 GLY A 851 5 5 SHEET 1 A 8 ASP A 249 ASP A 253 0 SHEET 2 A 8 THR A 277 LYS A 279 1 O THR A 277 N GLY A 250 SHEET 3 A 8 ARG A 293 TYR A 296 1 O ARG A 293 N TYR A 278 SHEET 4 A 8 LEU A 304 ALA A 307 -1 O TYR A 306 N PHE A 294 SHEET 5 A 8 VAL A 686 ASP A 690 1 O ASN A 687 N TYR A 305 SHEET 6 A 8 ARG A 667 ASN A 674 -1 N TYR A 670 O VAL A 686 SHEET 7 A 8 ASP A 639 SER A 645 -1 N MET A 642 O ALA A 671 SHEET 8 A 8 PHE A 633 VAL A 636 -1 N VAL A 636 O ASP A 639 SHEET 1 B 2 ILE A 271 ASN A 272 0 SHEET 2 B 2 PHE A 289 ILE A 290 1 O ILE A 290 N ILE A 271 SHEET 1 C 4 GLY A 314 LYS A 318 0 SHEET 2 C 4 ASP A 746 LYS A 753 -1 O CYS A 749 N PHE A 317 SHEET 3 C 4 TYR A 713 GLY A 720 -1 N ILE A 714 O MET A 752 SHEET 4 C 4 GLY A 703 LYS A 710 -1 N VAL A 708 O TYR A 715 SHEET 1 D 3 TYR A 325 ALA A 327 0 SHEET 2 D 3 VAL A 339 SER A 347 -1 O SER A 347 N TYR A 325 SHEET 3 D 3 PHE A 334 TYR A 336 -1 N PHE A 334 O TYR A 341 SHEET 1 E 4 TYR A 325 ALA A 327 0 SHEET 2 E 4 VAL A 339 SER A 347 -1 O SER A 347 N TYR A 325 SHEET 3 E 4 HIS A 356 SER A 362 -1 O VAL A 360 N ALA A 342 SHEET 4 E 4 GLU A 373 TRP A 374 -1 O GLU A 373 N TRP A 359 SHEET 1 F 3 VAL A 385 HIS A 388 0 SHEET 2 F 3 ARG A 398 THR A 407 -1 O GLU A 404 N HIS A 388 SHEET 3 F 3 MET A 392 CYS A 395 -1 N GLY A 393 O PHE A 400 SHEET 1 G 4 VAL A 385 HIS A 388 0 SHEET 2 G 4 ARG A 398 THR A 407 -1 O GLU A 404 N HIS A 388 SHEET 3 G 4 LEU A 413 PRO A 422 -1 O THR A 414 N THR A 405 SHEET 4 G 4 ARG A 513 GLY A 518 -1 O LEU A 517 N CYS A 416 SHEET 1 H 4 SER A 426 THR A 430 0 SHEET 2 H 4 ASN A 500 THR A 505 -1 O MET A 503 N LEU A 427 SHEET 3 H 4 PHE A 456 SER A 460 -1 N SER A 460 O HIS A 502 SHEET 4 H 4 GLY A 469 THR A 472 -1 O MET A 471 N VAL A 457 SHEET 1 I 5 THR A 475 ASP A 478 0 SHEET 2 I 5 ASN A 481 LEU A 485 -1 O THR A 483 N THR A 475 SHEET 3 I 5 TYR A 441 HIS A 445 -1 N ILE A 444 O PHE A 482 SHEET 4 I 5 ILE A 433 LYS A 435 -1 N THR A 434 O THR A 443 SHEET 5 I 5 LEU A 494 ASN A 495 -1 O LEU A 494 N LYS A 435 SHEET 1 J 4 GLU A 525 THR A 531 0 SHEET 2 J 4 PHE A 537 GLN A 543 -1 O ALA A 538 N ALA A 530 SHEET 3 J 4 GLU A 550 PHE A 556 -1 O PHE A 554 N MET A 539 SHEET 4 J 4 VAL A 567 GLN A 570 -1 O ARG A 569 N LEU A 553 SHEET 1 K 4 ALA A 579 TYR A 587 0 SHEET 2 K 4 VAL A 590 GLY A 597 -1 O TYR A 592 N LYS A 585 SHEET 3 K 4 SER A 606 SER A 610 -1 O SER A 610 N LEU A 591 SHEET 4 K 4 GLU A 618 ARG A 621 -1 O GLU A 618 N ARG A 609 SHEET 1 L 2 PHE A 777 PHE A 778 0 SHEET 2 L 2 ARG A 784 THR A 785 -1 O THR A 785 N PHE A 777 SHEET 1 M 3 ARG A 837 CYS A 841 0 SHEET 2 M 3 GLN A 853 TYR A 857 -1 O ILE A 854 N PHE A 840 SHEET 3 M 3 ILE A 867 ASN A 870 -1 O ASN A 870 N GLN A 853 LINK O8 SLB B 1 C2 SIA B 2 1555 1555 1.45 LINK O8 SIA B 2 C2 SIA B 3 1555 1555 1.45 LINK O8 SIA B 3 C2 SIA B 4 1555 1555 1.44 LINK O8 SIA B 4 C2 SIA B 5 1555 1555 1.43 LINK O8 SLB C 1 C2 SIA C 2 1555 1555 1.43 LINK O8 SIA C 2 C2 SIA C 3 1555 1555 1.44 LINK O8 SIA C 3 C2 SIA C 4 1555 1555 1.39 CISPEP 1 TYR A 382 PRO A 383 0 8.90 CISPEP 2 MET A 503 GLY A 504 0 -5.04 CISPEP 3 MET A 503 GLY A 504 0 -8.72 CISPEP 4 ALA A 547 PRO A 548 0 -2.34 CRYST1 119.090 119.090 175.980 90.00 90.00 120.00 H 3 9 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 0.008397 0.004848 0.000000 0.00000 SCALE2 0.000000 0.009696 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005682 0.00000