HEADER BIOSYNTHETIC PROTEIN,TRANSFERASE 08-JUL-19 6PPX TITLE CRYSTAL STRUCTURE OF METAL-FREE NEUB, AN N-ACETYLNEURAMINATE SYNTHASE TITLE 2 FROM NEISSERIA MENINGITIDIS IN COMPLEX WITH MALATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLNEURAMINATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SYNC PROTEIN; COMPND 5 EC: 2.5.1.56; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS SEROGROUP B; SOURCE 3 ORGANISM_TAXID: 491; SOURCE 4 GENE: SYNC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NEUB, TRANSFERASE, SIALIC ACID SYNTHASE, N-ACETYLNEURAMINATE KEYWDS 2 SYNTHASE, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.Z.ROSANALLY,M.S.JUNOP,P.J.BERTI REVDAT 5 11-OCT-23 6PPX 1 REMARK REVDAT 4 08-JAN-20 6PPX 1 REMARK REVDAT 3 23-OCT-19 6PPX 1 JRNL REVDAT 2 09-OCT-19 6PPX 1 SPRSDE REVDAT 1 02-OCT-19 6PPX 0 SPRSDE 09-OCT-19 6PPX 3CM4 JRNL AUTH V.POPOVIC,E.MORRISON,A.Z.ROSANALLY,N.BALACHANDRAN, JRNL AUTH 2 A.W.SENSON,R.SZABLA,M.S.JUNOP,P.J.BERTI JRNL TITL NEUNAC OXIME: A SLOW-BINDING AND EFFECTIVELY IRREVERSIBLE JRNL TITL 2 INHIBITOR OF THE SIALIC ACID SYNTHASE NEUB. JRNL REF BIOCHEMISTRY V. 58 4236 2019 JRNL REFN ISSN 0006-2960 JRNL PMID 31549502 JRNL DOI 10.1021/ACS.BIOCHEM.9B00654 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 29641 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1506 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 46.5000 - 4.1100 0.96 2657 146 0.1420 0.1680 REMARK 3 2 4.1100 - 3.2700 1.00 2616 153 0.1419 0.2069 REMARK 3 3 3.2700 - 2.8500 1.00 2615 121 0.1828 0.2478 REMARK 3 4 2.8500 - 2.5900 1.00 2605 128 0.1990 0.3068 REMARK 3 5 2.5900 - 2.4100 1.00 2553 152 0.1963 0.2596 REMARK 3 6 2.4100 - 2.2600 1.00 2584 125 0.2026 0.2740 REMARK 3 7 2.2600 - 2.1500 0.99 2517 140 0.2061 0.2851 REMARK 3 8 2.1500 - 2.0600 0.98 2540 125 0.2258 0.2728 REMARK 3 9 2.0600 - 1.9800 0.98 2485 145 0.2614 0.3241 REMARK 3 10 1.9800 - 1.9100 0.98 2494 139 0.3004 0.3268 REMARK 3 11 1.9100 - 1.8500 0.97 2469 132 0.3417 0.3769 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.286 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.70 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 : 0.007 2736 REMARK 3 ANGLE : 0.806 3691 REMARK 3 CHIRALITY : 0.052 408 REMARK 3 PLANARITY : 0.005 487 REMARK 3 DIHEDRAL : 28.947 1033 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6PPX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000242818. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29645 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 77.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.5300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.67300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 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: 1XUZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3% (V/V) MPD 1.75M MALIC ACID 10MM REMARK 280 MAGNESIUM CHLORIDE 10MM N-ACETYLNEURAMINIC ACID, PH 6.2, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 29.03500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.03500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.10000 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 -1.000000 0.000000 0.000000 58.07000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 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 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 218 -169.88 -160.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLT A 701 DBREF 6PPX A 1 349 UNP H2VFG5 H2VFG5_NEIMI 1 349 SEQRES 1 A 349 MET GLN ASN ASN ASN GLU PHE LYS ILE GLY ASN ARG SER SEQRES 2 A 349 VAL GLY TYR ASN HIS GLU PRO LEU ILE ILE CYS GLU ILE SEQRES 3 A 349 GLY ILE ASN HIS GLU GLY SER LEU LYS THR ALA PHE GLU SEQRES 4 A 349 MET VAL ASP ALA ALA TYR ASN ALA GLY ALA GLU VAL VAL SEQRES 5 A 349 LYS HIS GLN THR HIS ILE VAL GLU ASP GLU MET SER ASP SEQRES 6 A 349 GLU ALA LYS GLN VAL ILE PRO GLY ASN ALA ASP VAL SER SEQRES 7 A 349 ILE TYR GLU ILE MET GLU ARG CYS ALA LEU ASN GLU GLU SEQRES 8 A 349 ASP GLU ILE LYS LEU LYS GLU TYR VAL GLU SER LYS GLY SEQRES 9 A 349 MET ILE PHE ILE SER THR PRO PHE SER ARG ALA ALA ALA SEQRES 10 A 349 LEU ARG LEU GLN ARG MET ASP ILE PRO ALA TYR LYS ILE SEQRES 11 A 349 GLY SER GLY GLU CYS ASN ASN TYR PRO LEU ILE LYS LEU SEQRES 12 A 349 VAL ALA SER PHE GLY LYS PRO ILE ILE LEU SER THR GLY SEQRES 13 A 349 MET ASN SER ILE GLU SER ILE LYS LYS SER VAL GLU ILE SEQRES 14 A 349 ILE ARG GLU ALA GLY VAL PRO TYR ALA LEU LEU HIS CYS SEQRES 15 A 349 THR ASN ILE TYR PRO THR PRO TYR GLU ASP VAL ARG LEU SEQRES 16 A 349 GLY GLY MET ASN ASP LEU SER GLU ALA PHE PRO ASP ALA SEQRES 17 A 349 ILE ILE GLY LEU SER ASP HIS THR LEU ASP ASN TYR ALA SEQRES 18 A 349 CYS LEU GLY ALA VAL ALA LEU GLY GLY SER ILE LEU GLU SEQRES 19 A 349 ARG HIS PHE THR ASP ARG MET ASP ARG PRO GLY PRO ASP SEQRES 20 A 349 ILE VAL CYS SER MET ASN PRO ASP THR PHE LYS GLU LEU SEQRES 21 A 349 LYS GLN GLY ALA HIS ALA LEU LYS LEU ALA ARG GLY GLY SEQRES 22 A 349 LYS LYS ASP THR ILE ILE ALA GLY GLU LYS PRO THR LYS SEQRES 23 A 349 ASP PHE ALA PHE ALA SER VAL VAL ALA ASP LYS ASP ILE SEQRES 24 A 349 LYS LYS GLY GLU LEU LEU SER GLY ASP ASN LEU TRP VAL SEQRES 25 A 349 LYS ARG PRO GLY ASN GLY ASP PHE SER VAL ASN GLU TYR SEQRES 26 A 349 GLU THR LEU PHE GLY LYS VAL ALA ALA CYS ASN ILE ARG SEQRES 27 A 349 LYS GLY ALA GLN ILE LYS LYS THR ASP ILE GLU HET MLT A 701 13 HETNAM MLT D-MALATE HETSYN MLT (2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID FORMUL 2 MLT C4 H6 O5 FORMUL 3 HOH *339(H2 O) HELIX 1 AA1 SER A 33 ALA A 47 1 15 HELIX 2 AA2 ILE A 58 MET A 63 1 6 HELIX 3 AA3 SER A 64 VAL A 70 5 7 HELIX 4 AA4 SER A 78 ALA A 87 1 10 HELIX 5 AA5 ASN A 89 LYS A 103 1 15 HELIX 6 AA6 SER A 113 ASP A 124 1 12 HELIX 7 AA7 GLY A 131 CYS A 135 5 5 HELIX 8 AA8 ASN A 137 SER A 146 1 10 HELIX 9 AA9 SER A 159 GLY A 174 1 16 HELIX 10 AB1 PRO A 189 ARG A 194 5 6 HELIX 11 AB2 LEU A 195 PHE A 205 1 11 HELIX 12 AB3 ASN A 219 LEU A 228 1 10 HELIX 13 AB4 ASP A 247 SER A 251 5 5 HELIX 14 AB5 ASN A 253 ARG A 271 1 19 HELIX 15 AB6 ILE A 279 GLY A 281 5 3 HELIX 16 AB7 GLU A 282 PHE A 290 1 9 HELIX 17 AB8 SER A 321 PHE A 329 5 9 HELIX 18 AB9 LYS A 344 ILE A 348 5 5 SHEET 1 AA1 2 GLU A 6 ILE A 9 0 SHEET 2 AA1 2 ARG A 12 GLY A 15 -1 O VAL A 14 N PHE A 7 SHEET 1 AA2 8 ILE A 106 PRO A 111 0 SHEET 2 AA2 8 VAL A 51 THR A 56 1 N VAL A 52 O ILE A 106 SHEET 3 AA2 8 LEU A 21 GLY A 27 1 N CYS A 24 O LYS A 53 SHEET 4 AA2 8 ILE A 232 HIS A 236 1 O LEU A 233 N ILE A 23 SHEET 5 AA2 8 ILE A 209 SER A 213 1 N LEU A 212 O ILE A 232 SHEET 6 AA2 8 TYR A 177 HIS A 181 1 N HIS A 181 O SER A 213 SHEET 7 AA2 8 ILE A 151 SER A 154 1 N LEU A 153 O LEU A 180 SHEET 8 AA2 8 TYR A 128 ILE A 130 1 N TYR A 128 O ILE A 152 SHEET 1 AA3 2 SER A 292 ALA A 295 0 SHEET 2 AA3 2 LEU A 310 LYS A 313 -1 O LYS A 313 N SER A 292 CISPEP 1 TYR A 186 PRO A 187 0 -2.30 CISPEP 2 ARG A 314 PRO A 315 0 1.53 SITE 1 AC1 11 GLU A 25 LYS A 53 GLN A 55 THR A 110 SITE 2 AC1 11 PHE A 112 LYS A 129 GLY A 131 TYR A 186 SITE 3 AC1 11 HIS A 215 HIS A 236 HOH A 843 CRYST1 58.070 76.200 77.550 90.00 90.00 90.00 P 21 21 2 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 0.017221 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012895 0.00000