HEADER HYDROLASE(O-GLYCOSYL) 24-MAY-93 1SIL OBSLTE 31-AUG-94 1SIL 2SIL TITLE FIRST CRYSTAL STRUCTURE OF A BACTERIAL SIALIDASE SHOWS SAME TITLE 2 FOLD AS INFLUENZA VIRUS NEURAMINIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS HYDROLASE(O-GLYCOSYL) EXPDTA X-RAY DIFFRACTION AUTHOR S.J.CRENNELL,E.F.GARMAN,W.G.LAVER,E.R.VIMR,G.L.TAYLOR REVDAT 2 31-AUG-94 1SIL 3 OBSLTE REVDAT 1 31-OCT-93 1SIL 0 JRNL AUTH S.J.CRENNELL,E.F.GARMAN,W.G.LAVER,E.R.VIMR, JRNL AUTH 2 G.L.TAYLOR JRNL TITL FIRST CRYSTAL STRUCTURE OF A BACTERIAL SIALIDASE JRNL TITL 2 SHOWS SAME FOLD AS INFLUENZA VIRUS NEURAMINIDASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.TAYLOR,E.VIMR,E.GARMAN,G.LAVER REMARK 1 TITL PURIFICATION, CRYSTALLIZATION AND PRELIMINARY REMARK 1 TITL 2 CRYSTALLOGRAPHIC STUDY OF NEURAMINIDASE FROM REMARK 1 TITL 3 VIBRIO CHOLERAE AND SALMONELLA TYPHIMURIUM REMARK 1 REF J.MOL.BIOL. V. 226 1287 1992 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 1SIL REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2951 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 3.35 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SIL COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 1SIL DAN IS 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID REMARK 5 (DAMA). 1SIL REMARK 6 REMARK 6 1SIL THE AUTHORS ACKNOWLEDGE SEQUENCE DISCREPANCY WITH THE REMARK 6 1SIL SWISSPROT ENTRY NANH-SALTY, SIALIDASE (E.C.3.2.1.18). REMARK 6 THEY 1SIL STATE THAT SWISSPROT IS INCORRECT FROM RESIDUE REMARK 6 353 TO END 1SIL AND THAT THE GIVEN COORDINATES DESCRIBE THE REMARK 6 CORRECT 1SIL SEQUENCE. SEE ABOVE JRNL REFERENCE. 1SIL REMARK 7 REMARK 7 1SIL A FEW WATER MOLECULES APPEAR TO BE ASSOCIATED WITH A REMARK 7 1SIL DIFFERENT ASYMMETRIC UNIT. 1SIL REMARK 8 REMARK 8 1SIL CORRECTION. THIS ENTRY IS OBSOLETE. 31-AUG-94. 1SIL REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-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 23.75000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.10000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.10000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.75000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.25000 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 M RES CSSEQI PSI PHI REMARK 500 VAL 178 131.16 81.71 REMARK 500 SER 230 -30.12 45.37 REMARK 500 VAL 351 -100.24 51.24 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 821 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH 875 DISTANCE = 6.20 ANGSTROMS SEQRES 1 381 THR VAL GLU LYS SER VAL VAL PHE LYS ALA GLU GLY GLU SEQRES 2 381 HIS PHE THR ASP GLN LYS GLY ASN THR ILE VAL GLY SER SEQRES 3 381 GLY SER GLY GLY THR THR LYS TYR PHE ARG ILE PRO ALA SEQRES 4 381 MET CYS THR THR SER LYS GLY THR ILE VAL VAL PHE ALA SEQRES 5 381 ASP ALA ARG HIS ASN THR ALA SER ASP GLN SER PHE ILE SEQRES 6 381 ASP THR ALA ALA ALA ARG SER THR ASP GLY GLY LYS THR SEQRES 7 381 TRP ASN LYS LYS ILE ALA ILE TYR ASN ASP ARG VAL ASN SEQRES 8 381 SER LYS LEU SER ARG VAL MET ASP PRO THR CYS ILE VAL SEQRES 9 381 ALA ASN ILE GLN GLY ARG GLU THR ILE LEU VAL MET VAL SEQRES 10 381 GLY LYS TRP ASN ASN ASN ASP LYS THR TRP GLY ALA TYR SEQRES 11 381 ARG ASP LYS ALA PRO ASP THR ASP TRP ASP LEU VAL LEU SEQRES 12 381 TYR LYS SER THR ASP ASP GLY VAL THR PHE SER LYS VAL SEQRES 13 381 GLU THR ASN ILE HIS ASP ILE VAL THR LYS ASN GLY THR SEQRES 14 381 ILE SER ALA MET LEU GLY GLY VAL GLY SER GLY LEU GLN SEQRES 15 381 LEU ASN ASP GLY LYS LEU VAL PHE PRO VAL GLN MET VAL SEQRES 16 381 ARG THR LYS ASN ILE THR THR VAL LEU ASN THR SER PHE SEQRES 17 381 ILE TYR SER THR ASP GLY ILE THR TRP SER LEU PRO SER SEQRES 18 381 GLY TYR CYS GLU GLY PHE GLY SER GLU ASN ASN ILE ILE SEQRES 19 381 GLU PHE ASN ALA SER LEU VAL ASN ASN ILE ARG ASN SER SEQRES 20 381 GLY LEU ARG ARG SER PHE GLU THR LYS ASP PHE GLY LYS SEQRES 21 381 THR TRP THR GLU PHE PRO PRO MET ASP LYS LYS VAL ASP SEQRES 22 381 ASN ARG ASN HIS GLY VAL GLN GLY SER THR ILE THR ILE SEQRES 23 381 PRO SER GLY ASN LYS LEU VAL ALA ALA HIS SER SER ALA SEQRES 24 381 GLN ASN LYS ASN ASN ASP TYR THR ARG SER ASP ILE SER SEQRES 25 381 LEU TYR ALA HIS ASN LEU TYR SER GLY GLU VAL LYS LEU SEQRES 26 381 ILE ASP ALA PHE TYR PRO LYS VAL GLY ASN ALA SER GLY SEQRES 27 381 ALA GLY TYR SER CYS LEU SER TYR ARG LYS ASN VAL ASP SEQRES 28 381 LYS GLU THR LEU TYR VAL VAL TYR GLU ALA ASN GLY SER SEQRES 29 381 ILE GLU PHE GLN ASP LEU SER ARG HIS LEU PRO VAL ILE SEQRES 30 381 LYS SER TYR ASN FTNOTE 1 RESIDUE 136 IS A CIS PROLINE. HET DAN 800 20 HETNAM DAN 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID FORMUL 2 DAN C11 H17 N O8 FORMUL 3 HOH *140(H2 O1) HELIX 1 H1 ILE 161 ASN 168 1 8 HELIX 2 H2 SER 372 HIS 374 5 3 HELIX 3 H3 LEU 375 LYS 379 1 5 SHEET 1 B1 4 TYR 35 THR 43 0 SHEET 2 B1 4 ILE 49 ARG 56 -1 N VAL 50 O CYS 42 SHEET 3 B1 4 ILE 66 SER 73 -1 O ASP 67 N ALA 55 SHEET 4 B1 4 ASN 81 ILE 86 -1 O ASN 81 N ARG 72 SHEET 1 B2 4 ARG 97 ILE 108 0 SHEET 2 B2 4 ARG 111 TRP 121 -1 O ARG 111 N ILE 108 SHEET 3 B2 4 ASP 141 SER 147 -1 O ASP 141 N LYS 120 SHEET 4 B2 4 SER 155 LYS 156 -1 O SER 155 N LYS 146 SHEET 1 B3 4 ILE 171 GLY 176 0 SHEET 2 B3 4 LEU 189 ARG 197 -1 O GLN 194 N LEU 175 SHEET 3 B3 4 LEU 205 SER 212 -1 N ASN 206 O MET 195 SHEET 4 B3 4 CYS 225 GLU 226 -1 O CYS 225 N THR 207 SHEET 1 B4 4 ASN 232 PHE 237 0 SHEET 2 B4 4 SER 240 ILE 245 -1 O SER 240 N PHE 237 SHEET 3 B4 4 PHE 254 THR 256 -1 O THR 256 N LEU 241 SHEET 4 B4 4 THR 264 GLU 265 -1 N THR 264 O GLU 255 SHEET 1 B5 4 SER 283 SER 289 0 SHEET 2 B5 4 LYS 292 ALA 300 -1 O LYS 292 N SER 289 SHEET 3 B5 4 ILE 312 HIS 317 -1 O SER 313 N SER 299 SHEET 4 B5 4 VAL 324 TYR 331 -1 N LYS 325 O ALA 316 SHEET 1 B6 4 SER 343 ASN 350 0 SHEET 2 B6 4 LYS 353 ALA 362 -1 N THR 355 O ARG 348 SHEET 3 B6 4 SER 365 ASP 370 -1 N GLU 367 O TYR 360 SHEET 4 B6 4 LYS 5 PHE 9 -1 N SER 6 O PHE 368 TURN 1 T1 LYS 10 GLY 13 TURN 2 T2 ASP 18 GLY 21 TURN 3 T3 GLY 28 GLY 31 TURN 4 T4 THR 44 GLY 47 TURN 5 T5 ASN 92 LEU 95 TURN 6 T6 ILE 108 ARG 111 TURN 7 T7 THR 127 ALA 130 TURN 8 T8 ASP 137 TRP 140 TURN 9 T9 ASP 149 VAL 152 TURN 10 T10 LEU 184 GLY 187 TURN 11 T11 THR 198 ILE 201 TURN 12 T12 GLY 227 SER 230 TURN 13 T13 PHE 237 SER 240 TURN 14 T14 MET 269 LYS 272 TURN 15 T15 ARG 276 GLY 279 TURN 16 T16 SER 289 LYS 292 TURN 17 T17 ASN 302 ASN 305 TURN 18 T18 ASN 336 GLY 339 TURN 19 T19 ASN 350 LYS 353 TURN 20 T20 ALA 362 SER 365 SSBOND 1 CYS 42 CYS 103 CISPEP 1 ALA 135 PRO 136 0 -2.61 SITE 1 ACT 13 ARG 37 ARG 56 ASP 62 MET 99 SITE 2 ACT 13 ASP 100 TRP 121 TRP 128 LEU 175 SITE 3 ACT 13 GLU 231 ARG 246 ARG 309 TYR 342 SITE 4 ACT 13 GLU 361 CRYST1 47.500 82.500 92.200 90.00 90.00 90.00 P 21 21 21 4 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 0.021053 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012121 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010846 0.00000