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- PDB-2wqp: Crystal structure of sialic acid synthase NeuB-inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 2wqp
TitleCrystal structure of sialic acid synthase NeuB-inhibitor complex
ComponentsPOLYSIALIC ACID CAPSULE BIOSYNTHESIS PROTEIN SIAC
KeywordsTRANSFERASE / NEUB / INHIBITOR / TIM BARREL / SIALIC ACID SYNTHASE
Function / homology
Function and homology information


N-acylneuraminate-9-phosphate synthase activity / glycosylation / carbohydrate biosynthetic process / metal ion binding
Similarity search - Function
N-acetylneuraminic acid synthase, N-terminal / : / NeuB family / SAF domain / SAF / SAF domain / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. ...N-acetylneuraminic acid synthase, N-terminal / : / NeuB family / SAF domain / SAF / SAF domain / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / (2S)-2-hydroxybutanedioic acid / : / Chem-WQP / Polysialic acid capsule biosynthesis protein SiaC
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.75 Å
AuthorsLiu, F. / Lee, H.J. / Strynadka, N.C.J. / Tanner, M.E.
CitationJournal: Biochemistry / Year: 2009
Title: The Inhibition of Neisseria Meningitidis Sialic Acid Synthase by a Tetrahedral Intermediate Analog.
Authors: Liu, F. / Lee, H.J. / Strynadka, N.C.J. / Tanner, M.E.
History
DepositionAug 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 12, 2011Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYSIALIC ACID CAPSULE BIOSYNTHESIS PROTEIN SIAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7689
Polymers38,8811
Non-polymers8888
Water5,801322
1
A: POLYSIALIC ACID CAPSULE BIOSYNTHESIS PROTEIN SIAC
hetero molecules

A: POLYSIALIC ACID CAPSULE BIOSYNTHESIS PROTEIN SIAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,53718
Polymers77,7612
Non-polymers1,77516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,-y,z1
Buried area9950 Å2
ΔGint-39.78 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.619, 75.744, 77.361
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein POLYSIALIC ACID CAPSULE BIOSYNTHESIS PROTEIN SIAC / SYNC PROTEIN / SIALIC ACID SYNTHASE


Mass: 38880.723 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Strain: SEROGROUP B / Plasmid: PCWORI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q7DDU0

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Non-polymers , 6 types, 330 molecules

#2: Chemical ChemComp-WQP / 5-(ACETYLAMINO)-3,5-DIDEOXY-2-O-PHOSPHONO-D-ERYTHRO-L-MANNO-NONONIC ACID


Mass: 391.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22NO12P
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, PRO 111 TO LEU
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.2 / Details: 1.50-1.55 M MALIC ACID, PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979
DetectorType: BMC / Detector: CCD / Date: Jun 26, 2008 / Details: HIGH-RESOLUTION DOUBLE- CRYSTAL SAGITTAL FOCUSING
RadiationMonochromator: ROSENBAUM-ROCK MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 35158 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.4
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.2 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.692 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1754 5 %RANDOM
Rwork0.163 ---
obs0.165 33373 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2---1.13 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 55 322 3058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222782
X-RAY DIFFRACTIONr_bond_other_d0.0010.022530
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9863747
X-RAY DIFFRACTIONr_angle_other_deg0.63735928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5635351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60225.246122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2215495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7951513
X-RAY DIFFRACTIONr_chiral_restr0.0650.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213083
X-RAY DIFFRACTIONr_gen_planes_other00.02514
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4951.51733
X-RAY DIFFRACTIONr_mcbond_other0.1511.5715
X-RAY DIFFRACTIONr_mcangle_it0.91122784
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.94631049
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9434.5961
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 120 -
Rwork0.242 2371 -
obs--96.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.797-3.1692-0.459810.0820.21466.9934-0.3199-0.27710.24350.60350.0881-0.4144-0.24030.05220.23180.1074-0.0243-0.10540.08570.00730.1253107.0504-3.639561.8788
20.8157-0.11550.27961.66510.52630.8863-0.01960.03520.0845-0.0356-0.0137-0.2473-0.02530.09620.03330.0029-0.00510.00750.05390.02350.0807104.4516-12.801845.1371
31.71031.2011-0.39651.1281-0.31310.3942-0.01970.1029-0.171-0.058-0.0152-0.19910.10070.07850.03490.05210.02470.00550.07530.01270.0765102.0125-31.269846.6881
40.7687-0.1503-0.26340.8773-0.12270.819-0.0033-0.04830.02730.1391-0.0441-0.24650.03070.16420.04740.02770.0008-0.03840.04840.01180.0703106.9941-20.961957.599
51.1202-0.34060.25621.2722-0.23970.77340.0049-0.10430.05620.23580.0139-0.0210.00750.024-0.01880.063-0.0077-0.01130.0257-0.00590.011594.1146-12.159260.6852
60.4219-0.6912-0.22773.75831.46771.11770.02820.02090.0419-0.0792-0.0374-0.0884-0.0431-0.00330.00930.0047-0.0077-0.00090.04050.01890.037195.0608-5.003146.6249
72.7395-1.4653-1.82623.10781.60022.28070.1538-0.0190.12960.2761-0.16210.0985-0.1539-0.20950.00830.1151-0.01080.0410.0529-0.03030.030576.777937.850263.7216
82.3905-0.6366-1.70472.37291.37563.89010.1702-0.23660.19730.3301-0.14290.0852-0.17880.0143-0.02730.1422-0.03860.05290.0525-0.03650.0476.159341.281667.605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 11
2X-RAY DIFFRACTION2A12 - 56
3X-RAY DIFFRACTION3A57 - 99
4X-RAY DIFFRACTION4A100 - 160
5X-RAY DIFFRACTION5A161 - 233
6X-RAY DIFFRACTION6A234 - 279
7X-RAY DIFFRACTION7A280 - 308
8X-RAY DIFFRACTION8A309 - 349

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