HEADER HYDROLASE 05-JUN-23 8T27 TITLE CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS SIALIDASE (PG_0352) TITLE 2 D219A MUTANT BOUND TO 6'-SIALYLLACTOSE (ONLY NEU5AC VISIBLE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIALIDASE, PUTATIVE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS; SOURCE 3 ORGANISM_TAXID: 837; SOURCE 4 GENE: PG_0352; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE80L KEYWDS SIALIDASE, NEURAMINIDASE, CARBOHYDRATE BINDING, VIRULENCE FACTOR, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.D.CLARK,M.G.MALKOWSKI REVDAT 2 11-OCT-23 8T27 1 JRNL REVDAT 1 04-OCT-23 8T27 0 JRNL AUTH N.D.CLARK,C.PHAM,K.KURNIYATI,C.W.SZE,L.COLEMAN,Q.FU,S.ZHANG, JRNL AUTH 2 M.G.MALKOWSKI,C.LI JRNL TITL FUNCTIONAL AND STRUCTURAL ANALYSES REVEAL THAT A DUAL DOMAIN JRNL TITL 2 SIALIDASE PROTECTS BACTERIA FROM COMPLEMENT KILLING THROUGH JRNL TITL 3 DESIALYLATION OF COMPLEMENT FACTORS. JRNL REF PLOS PATHOG. V. 19 11674 2023 JRNL REFN ESSN 1553-7374 JRNL PMID 37747935 JRNL DOI 10.1371/JOURNAL.PPAT.1011674 REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 103477 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5276 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 41.6700 - 4.3800 1.00 3438 220 0.1460 0.1558 REMARK 3 2 4.3800 - 3.4800 1.00 3391 189 0.1267 0.1487 REMARK 3 3 3.4800 - 3.0400 1.00 3397 185 0.1446 0.1650 REMARK 3 4 3.0400 - 2.7600 0.99 3365 167 0.1497 0.1890 REMARK 3 5 2.7600 - 2.5600 0.99 3328 184 0.1526 0.1856 REMARK 3 6 2.5600 - 2.4100 0.99 3350 178 0.1453 0.1655 REMARK 3 7 2.4100 - 2.2900 0.99 3281 199 0.1425 0.1658 REMARK 3 8 2.2900 - 2.1900 0.99 3304 180 0.1409 0.1832 REMARK 3 9 2.1900 - 2.1100 0.98 3321 174 0.1467 0.1761 REMARK 3 10 2.1100 - 2.0300 0.98 3245 185 0.1468 0.1756 REMARK 3 11 2.0300 - 1.9700 0.98 3319 159 0.1435 0.1603 REMARK 3 12 1.9700 - 1.9100 0.98 3248 200 0.1414 0.1758 REMARK 3 13 1.9100 - 1.8600 0.98 3284 169 0.1456 0.1499 REMARK 3 14 1.8600 - 1.8200 0.98 3292 152 0.1574 0.1876 REMARK 3 15 1.8200 - 1.7800 0.98 3264 179 0.1647 0.1945 REMARK 3 16 1.7800 - 1.7400 0.98 3265 194 0.1786 0.2009 REMARK 3 17 1.7400 - 1.7000 0.98 3289 167 0.1889 0.2022 REMARK 3 18 1.7000 - 1.6700 0.97 3214 175 0.1824 0.2251 REMARK 3 19 1.6700 - 1.6400 0.97 3292 160 0.1827 0.2083 REMARK 3 20 1.6400 - 1.6200 0.97 3207 190 0.1851 0.2256 REMARK 3 21 1.6200 - 1.5900 0.97 3215 167 0.1913 0.2181 REMARK 3 22 1.5900 - 1.5600 0.97 3254 162 0.1961 0.2117 REMARK 3 23 1.5600 - 1.5400 0.97 3225 153 0.2017 0.2356 REMARK 3 24 1.5400 - 1.5200 0.96 3267 165 0.2072 0.2331 REMARK 3 25 1.5200 - 1.5000 0.96 3186 154 0.2241 0.2540 REMARK 3 26 1.5000 - 1.4800 0.96 3219 169 0.2350 0.2573 REMARK 3 27 1.4800 - 1.4600 0.96 3208 171 0.2474 0.2857 REMARK 3 28 1.4600 - 1.4400 0.96 3189 182 0.2610 0.2783 REMARK 3 29 1.4400 - 1.4300 0.96 3186 171 0.2774 0.2890 REMARK 3 30 1.4300 - 1.4100 0.94 3158 176 0.3000 0.2778 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.159 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.59 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 : 0.015 4423 REMARK 3 ANGLE : 1.463 6032 REMARK 3 CHIRALITY : 0.128 647 REMARK 3 PLANARITY : 0.014 808 REMARK 3 DIHEDRAL : 7.806 664 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 20 THROUGH 48 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9796 7.8637 14.6086 REMARK 3 T TENSOR REMARK 3 T11: 0.2072 T22: 0.2399 REMARK 3 T33: 0.2407 T12: 0.0337 REMARK 3 T13: -0.0324 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.7363 L22: 1.3492 REMARK 3 L33: 0.9442 L12: 0.5922 REMARK 3 L13: 0.4375 L23: 0.3149 REMARK 3 S TENSOR REMARK 3 S11: -0.1382 S12: 0.2700 S13: 0.1010 REMARK 3 S21: -0.1886 S22: 0.0511 S23: 0.1665 REMARK 3 S31: -0.0559 S32: -0.1125 S33: 0.0875 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 49 THROUGH 151 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.1604 16.7239 18.2553 REMARK 3 T TENSOR REMARK 3 T11: 0.1277 T22: 0.1277 REMARK 3 T33: 0.1725 T12: 0.0268 REMARK 3 T13: 0.0017 T23: 0.0110 REMARK 3 L TENSOR REMARK 3 L11: 3.8174 L22: 1.7729 REMARK 3 L33: 1.2936 L12: -1.1533 REMARK 3 L13: 1.0780 L23: -0.6993 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: -0.0231 S13: 0.2644 REMARK 3 S21: 0.0752 S22: -0.0097 S23: -0.0703 REMARK 3 S31: -0.0998 S32: -0.0884 S33: 0.0217 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 152 THROUGH 189 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.9246 9.1254 19.5296 REMARK 3 T TENSOR REMARK 3 T11: 0.1425 T22: 0.1122 REMARK 3 T33: 0.1890 T12: -0.0004 REMARK 3 T13: -0.0071 T23: 0.0207 REMARK 3 L TENSOR REMARK 3 L11: 3.0961 L22: 0.4857 REMARK 3 L33: 0.5791 L12: -0.8239 REMARK 3 L13: 0.3893 L23: -0.2648 REMARK 3 S TENSOR REMARK 3 S11: 0.0459 S12: -0.1428 S13: -0.0598 REMARK 3 S21: -0.0171 S22: 0.0535 S23: 0.1385 REMARK 3 S31: -0.0216 S32: -0.1206 S33: -0.1077 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 190 THROUGH 257 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.2672 2.4727 12.0665 REMARK 3 T TENSOR REMARK 3 T11: 0.1085 T22: 0.1087 REMARK 3 T33: 0.1310 T12: 0.0020 REMARK 3 T13: 0.0056 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 1.1148 L22: 1.1994 REMARK 3 L33: 2.5019 L12: 0.2445 REMARK 3 L13: 0.4039 L23: 0.5062 REMARK 3 S TENSOR REMARK 3 S11: 0.0011 S12: -0.0146 S13: 0.0733 REMARK 3 S21: -0.0648 S22: 0.0296 S23: -0.0275 REMARK 3 S31: -0.0861 S32: -0.0104 S33: -0.0292 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 258 THROUGH 363 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.6120 -12.6006 14.5847 REMARK 3 T TENSOR REMARK 3 T11: 0.1003 T22: 0.1187 REMARK 3 T33: 0.1237 T12: 0.0103 REMARK 3 T13: -0.0036 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 0.6933 L22: 0.9100 REMARK 3 L33: 1.0881 L12: 0.0304 REMARK 3 L13: 0.0701 L23: 0.4115 REMARK 3 S TENSOR REMARK 3 S11: 0.0149 S12: 0.0042 S13: -0.0210 REMARK 3 S21: -0.0253 S22: -0.0015 S23: -0.0708 REMARK 3 S31: 0.0458 S32: 0.0801 S33: -0.0191 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 364 THROUGH 436 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.4954 -19.3516 26.1990 REMARK 3 T TENSOR REMARK 3 T11: 0.1472 T22: 0.1052 REMARK 3 T33: 0.1283 T12: 0.0036 REMARK 3 T13: -0.0081 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 2.6397 L22: 1.0379 REMARK 3 L33: 0.9983 L12: 0.0937 REMARK 3 L13: -0.1333 L23: -0.0785 REMARK 3 S TENSOR REMARK 3 S11: -0.0316 S12: -0.0685 S13: -0.1796 REMARK 3 S21: 0.0701 S22: 0.0239 S23: 0.0308 REMARK 3 S31: 0.1205 S32: 0.0104 S33: 0.0001 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 437 THROUGH 523 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.0869 -4.7405 30.3979 REMARK 3 T TENSOR REMARK 3 T11: 0.1012 T22: 0.1293 REMARK 3 T33: 0.1109 T12: 0.0026 REMARK 3 T13: 0.0116 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.7663 L22: 1.9583 REMARK 3 L33: 1.8209 L12: -0.3018 REMARK 3 L13: -0.1194 L23: -0.7602 REMARK 3 S TENSOR REMARK 3 S11: 0.0079 S12: -0.0773 S13: -0.0140 REMARK 3 S21: 0.1976 S22: 0.0293 S23: 0.0976 REMARK 3 S31: -0.0210 S32: -0.0309 S33: -0.0350 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 8T27 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000275063. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0333 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS 3.8, XIA2 3.8.6 REMARK 200 DATA SCALING SOFTWARE : XIA2 3.8.6 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 103559 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410 REMARK 200 RESOLUTION RANGE LOW (A) : 41.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.07685 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.98880 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.040 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.2 REMARK 200 STARTING MODEL: 8FEB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM CITRATE TRIBASIC, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 28.39550 REMARK 290 SMTRY3 2 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 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 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 MET A 18 REMARK 465 ARG A 19 REMARK 465 VAL A 524 REMARK 465 ARG A 525 REMARK 465 GLN A 526 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 HIS A 24 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 29 OG REMARK 470 MET A 30 CG SD CE REMARK 470 GLU A 32 CG CD OE1 OE2 REMARK 470 GLU A 58 CD OE1 OE2 REMARK 470 LYS A 65 CD CE NZ REMARK 470 LYS A 75 CG CD CE NZ REMARK 470 GLU A 79 CD OE1 OE2 REMARK 470 LYS A 80 CE NZ REMARK 470 VAL A 140 CG1 CG2 REMARK 470 SER A 144 OG REMARK 470 SER A 146 OG REMARK 470 ARG A 161 CD NE CZ NH1 NH2 REMARK 470 LYS A 236 CD CE NZ REMARK 470 ARG A 284 NE CZ NH1 NH2 REMARK 470 LYS A 442 CE NZ REMARK 470 ARG A 474 NH1 NH2 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 ASP A 211 CB - CG - OD1 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 ALA A 83 149.76 -170.37 REMARK 500 SER A 172 98.25 -162.51 REMARK 500 ILE A 195 69.11 79.92 REMARK 500 TYR A 354 67.43 -105.58 REMARK 500 ASP A 381 -158.94 -170.36 REMARK 500 GLU A 404 -124.95 52.19 REMARK 500 GLU A 404 -125.70 52.19 REMARK 500 ASP A 462 79.86 72.08 REMARK 500 ASP A 462 79.86 62.15 REMARK 500 ALA A 487 -118.34 -130.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8FEB RELATED DB: PDB REMARK 900 UNLIGANDED STRUCTURE REMARK 900 RELATED ID: 8T1Y RELATED DB: PDB REMARK 900 NEU5AC2EN (DANA) BOUND STRUCTURE REMARK 900 RELATED ID: 8T1Z RELATED DB: PDB REMARK 900 NEU5AC (NANA) BOUND STRUCTURE REMARK 900 RELATED ID: 8T24 RELATED DB: PDB REMARK 900 UNLIGANDED SIALIDASE, FRUCTOSE IN CBM REMARK 900 RELATED ID: 8T26 RELATED DB: PDB REMARK 900 3'-SIALYLLACTOSE BOUND STRUCTURE (ONLY NEU5AC VISIBLE) DBREF 8T27 A 31 526 UNP Q7MX62 Q7MX62_PORGI 31 526 SEQADV 8T27 MET A 18 UNP Q7MX62 EXPRESSION TAG SEQADV 8T27 ARG A 19 UNP Q7MX62 EXPRESSION TAG SEQADV 8T27 GLY A 20 UNP Q7MX62 EXPRESSION TAG SEQADV 8T27 SER A 21 UNP Q7MX62 EXPRESSION TAG SEQADV 8T27 HIS A 22 UNP Q7MX62 EXPRESSION TAG SEQADV 8T27 HIS A 23 UNP Q7MX62 EXPRESSION TAG SEQADV 8T27 HIS A 24 UNP Q7MX62 EXPRESSION TAG SEQADV 8T27 HIS A 25 UNP Q7MX62 EXPRESSION TAG SEQADV 8T27 HIS A 26 UNP Q7MX62 EXPRESSION TAG SEQADV 8T27 HIS A 27 UNP Q7MX62 EXPRESSION TAG SEQADV 8T27 GLY A 28 UNP Q7MX62 EXPRESSION TAG SEQADV 8T27 SER A 29 UNP Q7MX62 EXPRESSION TAG SEQADV 8T27 MET A 30 UNP Q7MX62 EXPRESSION TAG SEQADV 8T27 ALA A 219 UNP Q7MX62 ASP 219 ENGINEERED MUTATION SEQRES 1 A 509 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER MET SEQRES 2 A 509 GLN GLU VAL THR MET TRP GLY ASP SER HIS GLY VAL ALA SEQRES 3 A 509 PRO ASN GLN VAL ARG ARG THR LEU VAL LYS VAL ALA LEU SEQRES 4 A 509 SER GLU SER LEU PRO PRO GLY ALA LYS GLN ILE ARG ILE SEQRES 5 A 509 GLY PHE SER LEU PRO LYS GLU THR GLU GLU LYS VAL THR SEQRES 6 A 509 ALA LEU TYR LEU LEU VAL SER ASP SER LEU ALA VAL ARG SEQRES 7 A 509 ASP LEU PRO ASP TYR LYS GLY ARG VAL SER TYR ASP SER SEQRES 8 A 509 PHE PRO ILE SER LYS GLU ASP ARG THR THR ALA LEU SER SEQRES 9 A 509 ALA ASP SER VAL ALA GLY ARG ARG PHE PHE TYR LEU ALA SEQRES 10 A 509 ALA ASP ILE GLY PRO VAL ALA SER PHE SER ARG SER ASP SEQRES 11 A 509 THR LEU THR ALA ARG VAL GLU GLU VAL ALA VAL ASP GLY SEQRES 12 A 509 ARG PRO LEU PRO LEU LYS GLU LEU SER PRO ALA SER ARG SEQRES 13 A 509 ARG LEU TYR ARG GLY TYR GLU ALA LEU PHE VAL PRO GLY SEQRES 14 A 509 ASP GLY GLY SER ARG ASN TYR ARG ILE PRO ALA ILE LEU SEQRES 15 A 509 LYS THR ALA ASN GLY THR LEU ILE ALA MET ALA ASP ARG SEQRES 16 A 509 ARG LYS TYR ASN GLN THR ALA LEU PRO GLU ASP ILE ASP SEQRES 17 A 509 ILE VAL MET ARG ARG SER THR ASP GLY GLY LYS SER TRP SEQRES 18 A 509 SER ASP PRO ARG ILE ILE VAL GLN GLY GLU GLY ARG ASN SEQRES 19 A 509 HIS GLY PHE GLY ASP VAL ALA LEU VAL GLN THR GLN ALA SEQRES 20 A 509 GLY LYS LEU LEU MET ILE PHE VAL GLY GLY VAL GLY LEU SEQRES 21 A 509 TRP GLN SER THR PRO ASP ARG PRO GLN ARG THR TYR ILE SEQRES 22 A 509 SER GLU SER ARG ASP GLU GLY LEU THR TRP SER PRO PRO SEQRES 23 A 509 ARG ASP ILE THR HIS PHE ILE PHE GLY LYS ASP CYS ALA SEQRES 24 A 509 ASP PRO GLY ARG SER ARG TRP LEU ALA SER PHE CYS ALA SEQRES 25 A 509 SER GLY GLN GLY LEU VAL LEU PRO SER GLY ARG ILE THR SEQRES 26 A 509 PHE VAL ALA ALA ILE ARG GLU SER GLY GLN GLU TYR VAL SEQRES 27 A 509 LEU ASN ASN TYR VAL LEU TYR SER ASP ASP GLU GLY ASP SEQRES 28 A 509 THR TRP GLN LEU SER ASP CYS ALA TYR ARG ARG GLY ASP SEQRES 29 A 509 GLU ALA LYS LEU SER LEU MET PRO ASP GLY ARG VAL LEU SEQRES 30 A 509 MET SER ILE ARG ASN GLN GLY ARG GLN GLU SER ARG GLN SEQRES 31 A 509 ARG PHE PHE ALA LEU SER SER ASP ASP GLY LEU THR TRP SEQRES 32 A 509 GLU ARG ALA LYS GLN PHE GLU GLY ILE HIS ASP PRO GLY SEQRES 33 A 509 CYS ASN GLY ALA MET LEU GLN VAL LYS ARG ASN GLY ARG SEQRES 34 A 509 ASP GLN VAL LEU HIS SER LEU PRO LEU GLY PRO ASP GLY SEQRES 35 A 509 ARG ARG ASP GLY ALA VAL TYR LEU PHE ASP HIS VAL SER SEQRES 36 A 509 GLY ARG TRP SER ALA PRO VAL VAL VAL ASN SER GLY SER SEQRES 37 A 509 SER ALA TYR SER ASP MET THR LEU LEU ALA ASP GLY THR SEQRES 38 A 509 ILE GLY TYR PHE VAL GLU GLU GLY ASP GLU ILE SER LEU SEQRES 39 A 509 VAL PHE ILE ARG PHE VAL LEU ASP ASP LEU PHE ASP VAL SEQRES 40 A 509 ARG GLN HET SIA A 601 21 HET PEG A 602 7 HET PGE A 603 10 HET EDO A 604 4 HET PEG A 605 7 HET GAL A 606 12 HET GAL A 607 12 HET PGE A 608 10 HET GAL A 609 12 HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PGE TRIETHYLENE GLYCOL HETNAM EDO 1,2-ETHANEDIOL HETNAM GAL BETA-D-GALACTOPYRANOSE HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID HETSYN EDO ETHYLENE GLYCOL HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 2 SIA C11 H19 N O9 FORMUL 3 PEG 2(C4 H10 O3) FORMUL 4 PGE 2(C6 H14 O4) FORMUL 5 EDO C2 H6 O2 FORMUL 7 GAL 3(C6 H12 O6) FORMUL 11 HOH *468(H2 O) HELIX 1 AA1 PRO A 74 GLU A 79 1 6 HELIX 2 AA2 ASP A 96 LYS A 101 5 6 HELIX 3 AA3 ALA A 122 ALA A 126 1 5 HELIX 4 AA4 GLY A 186 SER A 190 5 5 HELIX 5 AA5 THR A 307 ILE A 310 5 4 HELIX 6 AA6 ASP A 317 SER A 321 5 5 HELIX 7 AA7 LYS A 424 GLU A 427 5 4 HELIX 8 AA8 VAL A 517 ASP A 523 1 7 SHEET 1 AA1 6 TYR A 106 ILE A 111 0 SHEET 2 AA1 6 VAL A 81 SER A 89 -1 N LEU A 86 O PHE A 109 SHEET 3 AA1 6 PHE A 130 ILE A 137 -1 O TYR A 132 N LEU A 87 SHEET 4 AA1 6 ARG A 49 LEU A 56 -1 N LEU A 51 O LEU A 133 SHEET 5 AA1 6 VAL A 33 GLY A 37 -1 N THR A 34 O ALA A 55 SHEET 6 AA1 6 LEU A 165 GLU A 167 1 O LYS A 166 N MET A 35 SHEET 1 AA2 4 THR A 117 SER A 121 0 SHEET 2 AA2 4 GLN A 66 SER A 72 -1 N ILE A 69 O THR A 118 SHEET 3 AA2 4 ARG A 152 VAL A 158 -1 O ALA A 157 N ARG A 68 SHEET 4 AA2 4 ARG A 161 PRO A 162 -1 O ARG A 161 N VAL A 158 SHEET 1 AA3 2 THR A 148 LEU A 149 0 SHEET 2 AA3 2 ARG A 173 ARG A 174 -1 O ARG A 173 N LEU A 149 SHEET 1 AA4 7 GLY A 178 PHE A 183 0 SHEET 2 AA4 7 SER A 510 PHE A 516 -1 O PHE A 513 N GLU A 180 SHEET 3 AA4 7 ILE A 499 GLU A 505 -1 N TYR A 501 O ILE A 514 SHEET 4 AA4 7 VAL A 479 LEU A 493 -1 N ASP A 490 O PHE A 502 SHEET 5 AA4 7 ARG A 461 ASP A 469 -1 N ASP A 462 O GLY A 484 SHEET 6 AA4 7 ARG A 446 PRO A 454 -1 N HIS A 451 O TYR A 466 SHEET 7 AA4 7 ALA A 437 ARG A 443 -1 N LEU A 439 O LEU A 450 SHEET 1 AA5 6 GLY A 178 PHE A 183 0 SHEET 2 AA5 6 SER A 510 PHE A 516 -1 O PHE A 513 N GLU A 180 SHEET 3 AA5 6 ILE A 499 GLU A 505 -1 N TYR A 501 O ILE A 514 SHEET 4 AA5 6 VAL A 479 LEU A 493 -1 N ASP A 490 O PHE A 502 SHEET 5 AA5 6 ARG A 461 ASP A 469 -1 N ASP A 462 O GLY A 484 SHEET 6 AA5 6 ARG A 474 TRP A 475 -1 O ARG A 474 N ASP A 469 SHEET 1 AA6 4 ASN A 192 LYS A 200 0 SHEET 2 AA6 4 LEU A 206 ARG A 213 -1 O ASP A 211 N ARG A 194 SHEET 3 AA6 4 ASP A 225 SER A 231 -1 O ARG A 229 N ALA A 208 SHEET 4 AA6 4 ARG A 242 VAL A 245 -1 O VAL A 245 N ILE A 226 SHEET 1 AA7 5 ARG A 304 ASP A 305 0 SHEET 2 AA7 5 ARG A 287 SER A 293 -1 N ILE A 290 O ARG A 304 SHEET 3 AA7 5 LEU A 267 GLY A 273 -1 N LEU A 267 O SER A 293 SHEET 4 AA7 5 PHE A 254 GLN A 261 -1 N VAL A 260 O LEU A 268 SHEET 5 AA7 5 GLY A 331 GLN A 332 1 O GLY A 331 N VAL A 257 SHEET 1 AA8 3 ALA A 325 CYS A 328 0 SHEET 2 AA8 3 ILE A 341 ARG A 348 -1 O ARG A 348 N ALA A 325 SHEET 3 AA8 3 LEU A 334 VAL A 335 -1 N LEU A 334 O THR A 342 SHEET 1 AA9 4 ALA A 325 CYS A 328 0 SHEET 2 AA9 4 ILE A 341 ARG A 348 -1 O ARG A 348 N ALA A 325 SHEET 3 AA9 4 LEU A 356 SER A 363 -1 O LEU A 361 N PHE A 343 SHEET 4 AA9 4 GLN A 371 GLY A 380 -1 O ALA A 376 N ASN A 358 SHEET 1 AB1 4 ALA A 383 LEU A 387 0 SHEET 2 AB1 4 VAL A 393 ILE A 397 -1 O LEU A 394 N SER A 386 SHEET 3 AB1 4 PHE A 409 SER A 413 -1 O PHE A 409 N ILE A 397 SHEET 4 AB1 4 GLU A 421 ARG A 422 -1 O GLU A 421 N LEU A 412 CISPEP 1 LEU A 220 PRO A 221 0 18.79 CISPEP 2 GLY A 456 PRO A 457 0 6.77 CRYST1 61.717 56.791 80.137 90.00 96.33 90.00 P 1 21 1 2 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 0.016203 0.000000 0.001797 0.00000 SCALE2 0.000000 0.017608 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012555 0.00000