HEADER HYDROLASE 05-JUN-23 8T26 TITLE CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS SIALIDASE (PG_0352) TITLE 2 D219A MUTANT BOUND TO 3'-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 8T26 1 JRNL REVDAT 1 04-OCT-23 8T26 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. 1.42 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 103081 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 5321 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 46.0800 - 4.4100 1.00 3377 188 0.1566 0.1727 REMARK 3 2 4.4100 - 3.5000 1.00 3319 188 0.1355 0.1490 REMARK 3 3 3.5000 - 3.0600 1.00 3284 190 0.1496 0.1758 REMARK 3 4 3.0600 - 2.7800 1.00 3280 168 0.1576 0.1872 REMARK 3 5 2.7800 - 2.5800 1.00 3269 178 0.1554 0.1743 REMARK 3 6 2.5800 - 2.4300 1.00 3310 180 0.1472 0.1474 REMARK 3 7 2.4300 - 2.3100 1.00 3266 180 0.1480 0.1935 REMARK 3 8 2.3100 - 2.2100 1.00 3270 181 0.1422 0.1583 REMARK 3 9 2.2100 - 2.1200 1.00 3248 173 0.1487 0.1693 REMARK 3 10 2.1200 - 2.0500 1.00 3242 180 0.1507 0.1960 REMARK 3 11 2.0500 - 1.9900 1.00 3303 162 0.1506 0.1603 REMARK 3 12 1.9900 - 1.9300 1.00 3268 169 0.1492 0.1752 REMARK 3 13 1.9300 - 1.8800 1.00 3242 186 0.1481 0.1789 REMARK 3 14 1.8800 - 1.8300 1.00 3277 154 0.1598 0.2125 REMARK 3 15 1.8300 - 1.7900 1.00 3247 178 0.1747 0.2213 REMARK 3 16 1.7900 - 1.7500 1.00 3278 192 0.1800 0.2370 REMARK 3 17 1.7500 - 1.7200 1.00 3214 176 0.1791 0.2252 REMARK 3 18 1.7200 - 1.6800 1.00 3294 171 0.1874 0.2123 REMARK 3 19 1.6800 - 1.6500 1.00 3243 176 0.1859 0.2256 REMARK 3 20 1.6500 - 1.6300 1.00 3241 197 0.1875 0.2216 REMARK 3 21 1.6300 - 1.6000 1.00 3247 179 0.1919 0.2148 REMARK 3 22 1.6000 - 1.5800 1.00 3196 177 0.1948 0.2123 REMARK 3 23 1.5800 - 1.5500 1.00 3304 173 0.2044 0.2003 REMARK 3 24 1.5500 - 1.5300 1.00 3212 168 0.2145 0.2694 REMARK 3 25 1.5300 - 1.5100 1.00 3244 198 0.2287 0.2440 REMARK 3 26 1.5100 - 1.4900 1.00 3227 172 0.2497 0.2999 REMARK 3 27 1.4900 - 1.4700 1.00 3255 170 0.2556 0.2582 REMARK 3 28 1.4700 - 1.4500 0.99 3198 185 0.2718 0.3054 REMARK 3 29 1.4500 - 1.4400 0.99 3233 177 0.2937 0.3279 REMARK 3 30 1.4400 - 1.4200 0.98 3172 155 0.3130 0.3389 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) : 0.178 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.678 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.67 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 : 0.009 4465 REMARK 3 ANGLE : 1.108 6100 REMARK 3 CHIRALITY : 0.109 640 REMARK 3 PLANARITY : 0.012 831 REMARK 3 DIHEDRAL : 9.070 684 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 20 THROUGH 48 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.5639 7.7971 14.0759 REMARK 3 T TENSOR REMARK 3 T11: 0.2510 T22: 0.2732 REMARK 3 T33: 0.2711 T12: 0.0325 REMARK 3 T13: -0.0273 T23: 0.0123 REMARK 3 L TENSOR REMARK 3 L11: 1.9427 L22: 0.5748 REMARK 3 L33: 0.5260 L12: 0.4433 REMARK 3 L13: 0.6567 L23: 0.2179 REMARK 3 S TENSOR REMARK 3 S11: -0.1835 S12: 0.2368 S13: 0.2002 REMARK 3 S21: -0.1166 S22: 0.0647 S23: 0.1268 REMARK 3 S31: -0.1233 S32: -0.0557 S33: 0.1214 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 49 THROUGH 151 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.6858 16.8426 17.9026 REMARK 3 T TENSOR REMARK 3 T11: 0.1326 T22: 0.1362 REMARK 3 T33: 0.1601 T12: 0.0323 REMARK 3 T13: 0.0094 T23: 0.0076 REMARK 3 L TENSOR REMARK 3 L11: 4.0100 L22: 1.9067 REMARK 3 L33: 1.0889 L12: -1.1548 REMARK 3 L13: 1.1289 L23: -0.6026 REMARK 3 S TENSOR REMARK 3 S11: -0.0481 S12: -0.0908 S13: 0.2494 REMARK 3 S21: 0.1083 S22: 0.0255 S23: -0.0541 REMARK 3 S31: -0.0680 S32: -0.1001 S33: 0.0210 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 152 THROUGH 189 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.5464 9.2581 19.6653 REMARK 3 T TENSOR REMARK 3 T11: 0.1362 T22: 0.0915 REMARK 3 T33: 0.1653 T12: 0.0078 REMARK 3 T13: 0.0052 T23: 0.0167 REMARK 3 L TENSOR REMARK 3 L11: 3.4828 L22: 0.4892 REMARK 3 L33: 0.6526 L12: -0.8673 REMARK 3 L13: 0.4250 L23: -0.3317 REMARK 3 S TENSOR REMARK 3 S11: 0.0261 S12: -0.1680 S13: -0.0990 REMARK 3 S21: 0.0038 S22: 0.0719 S23: 0.1403 REMARK 3 S31: -0.0578 S32: -0.1636 S33: -0.1050 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 190 THROUGH 363 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.6968 -6.4333 13.5743 REMARK 3 T TENSOR REMARK 3 T11: 0.1043 T22: 0.1191 REMARK 3 T33: 0.1162 T12: -0.0044 REMARK 3 T13: 0.0078 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 0.5668 L22: 0.7447 REMARK 3 L33: 0.8060 L12: -0.1321 REMARK 3 L13: -0.0182 L23: 0.0222 REMARK 3 S TENSOR REMARK 3 S11: 0.0126 S12: 0.0058 S13: 0.0093 REMARK 3 S21: -0.0278 S22: 0.0135 S23: -0.0632 REMARK 3 S31: -0.0038 S32: 0.0528 S33: -0.0257 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 364 THROUGH 436 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.5294 -19.2530 26.1959 REMARK 3 T TENSOR REMARK 3 T11: 0.1311 T22: 0.0805 REMARK 3 T33: 0.1044 T12: 0.0042 REMARK 3 T13: -0.0004 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 3.4407 L22: 1.2372 REMARK 3 L33: 1.2017 L12: 0.3195 REMARK 3 L13: 0.0916 L23: -0.0581 REMARK 3 S TENSOR REMARK 3 S11: 0.0065 S12: -0.1021 S13: -0.1985 REMARK 3 S21: 0.0743 S22: 0.0023 S23: 0.0335 REMARK 3 S31: 0.1436 S32: 0.0076 S33: -0.0119 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 437 THROUGH 523 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.8657 -4.9449 30.2465 REMARK 3 T TENSOR REMARK 3 T11: 0.0886 T22: 0.1048 REMARK 3 T33: 0.0942 T12: 0.0018 REMARK 3 T13: 0.0230 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 1.1962 L22: 1.9177 REMARK 3 L33: 2.9464 L12: -0.3345 REMARK 3 L13: 0.1083 L23: -0.8165 REMARK 3 S TENSOR REMARK 3 S11: 0.0110 S12: -0.0857 S13: -0.0234 REMARK 3 S21: 0.1903 S22: 0.0203 S23: 0.0877 REMARK 3 S31: 0.0056 S32: -0.0475 S33: -0.0286 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 8T26 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_1000275061. 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, XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 103256 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 46.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.11830 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.96580 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.850 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: 8FEB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 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 28.41450 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 GLU A 32 CD OE1 OE2 REMARK 470 LYS A 65 CD CE NZ REMARK 470 LYS A 75 CG CD CE NZ REMARK 470 LYS A 80 CE NZ REMARK 470 VAL A 140 CG1 CG2 REMARK 470 SER A 144 OG REMARK 470 ARG A 161 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 236 CE NZ REMARK 470 ARG A 284 NE CZ NH1 NH2 REMARK 470 LYS A 442 CE NZ REMARK 470 ASP A 523 CG OD1 OD2 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 LEU A 73 115.20 -161.75 REMARK 500 SER A 172 95.30 -162.69 REMARK 500 SER A 172 90.46 -164.85 REMARK 500 TYR A 179 116.75 -160.04 REMARK 500 ILE A 195 71.52 75.48 REMARK 500 ASN A 216 -179.73 -179.35 REMARK 500 ASP A 256 65.48 60.50 REMARK 500 TYR A 354 66.69 -101.04 REMARK 500 ASP A 381 -157.03 -168.28 REMARK 500 GLU A 404 -125.84 52.43 REMARK 500 ASP A 462 82.52 66.36 REMARK 500 ASP A 462 82.52 62.77 REMARK 500 ALA A 487 -118.49 -131.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 322 0.11 SIDE CHAIN 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 DOMAIN, FRUCTOSE-BOUND CBM DBREF 8T26 A 31 526 UNP Q7MX62 Q7MX62_PORGI 31 526 SEQADV 8T26 MET A 18 UNP Q7MX62 EXPRESSION TAG SEQADV 8T26 ARG A 19 UNP Q7MX62 EXPRESSION TAG SEQADV 8T26 GLY A 20 UNP Q7MX62 EXPRESSION TAG SEQADV 8T26 SER A 21 UNP Q7MX62 EXPRESSION TAG SEQADV 8T26 HIS A 22 UNP Q7MX62 EXPRESSION TAG SEQADV 8T26 HIS A 23 UNP Q7MX62 EXPRESSION TAG SEQADV 8T26 HIS A 24 UNP Q7MX62 EXPRESSION TAG SEQADV 8T26 HIS A 25 UNP Q7MX62 EXPRESSION TAG SEQADV 8T26 HIS A 26 UNP Q7MX62 EXPRESSION TAG SEQADV 8T26 HIS A 27 UNP Q7MX62 EXPRESSION TAG SEQADV 8T26 GLY A 28 UNP Q7MX62 EXPRESSION TAG SEQADV 8T26 SER A 29 UNP Q7MX62 EXPRESSION TAG SEQADV 8T26 MET A 30 UNP Q7MX62 EXPRESSION TAG SEQADV 8T26 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 PGE A 604 10 HET GAL A 605 12 HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PGE TRIETHYLENE GLYCOL HETNAM GAL BETA-D-GALACTOPYRANOSE HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE FORMUL 2 SIA C11 H19 N O9 FORMUL 3 PEG C4 H10 O3 FORMUL 4 PGE 2(C6 H14 O4) FORMUL 6 GAL C6 H12 O6 FORMUL 7 HOH *489(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 84 O ILE A 111 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 SER A 169 1 O LEU A 168 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 ILE A 499 O PHE A 516 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 VAL A 449 O PHE A 468 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 ILE A 499 O PHE A 516 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 ASP A 225 N ARG A 212 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 ALA A 411 N MET A 395 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 18.20 CISPEP 2 GLY A 456 PRO A 457 0 6.76 CRYST1 61.484 56.829 80.026 90.00 96.30 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 0.016264 0.000000 0.001796 0.00000 SCALE2 0.000000 0.017597 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012572 0.00000