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- PDB-4ipi: Crystal Structure of R314A N-acetyl Neuraminic Acid Synthase from... -

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Basic information

Entry
Database: PDB / ID: 4ipi
TitleCrystal Structure of R314A N-acetyl Neuraminic Acid Synthase from Neiserria meningitidis with Malate bound
ComponentsPolysialic acid capsule biosynthesis protein SiaC
KeywordsTRANSFERASE / Antifreeze Protein Fold / NANA / N-acetylneuraminic acid / sialic acid / Neisseria meningitidis
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 domain / SAF / 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 ...N-acetylneuraminic acid synthase, N-terminal / NeuB family / SAF domain / SAF domain / SAF / 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
(2S)-2-hydroxybutanedioic acid / : / Capsule biosynthesis protein / Polysialic acid capsule biosynthesis protein SiaC
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJoseph, D.D.A. / Jiao, W. / Parker, E.J.
CitationJournal: Biochemistry / Year: 2013
Title: Arg314 Is Essential for Catalysis by N-Acetyl Neuraminic Acid Synthase from Neisseria meningitidis.
Authors: Joseph, D.D. / Jiao, W. / Parker, E.J.
History
DepositionJan 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Polysialic acid capsule biosynthesis protein SiaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7614
Polymers38,4381
Non-polymers3233
Water6,395355
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)77,5228
Polymers76,8752
Non-polymers6466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,-y,z1
Buried area7460 Å2
ΔGint-56 kcal/mol
Surface area26370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.000, 75.800, 77.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Polysialic acid capsule biosynthesis protein SiaC / N-Acetyl Neuraminic Acid Synthase


Mass: 38437.742 Da / Num. of mol.: 1 / Mutation: R314A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: siaC, NMB0068 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7DDU0, UniProt: Q57265*PLUS, N-acetylneuraminate synthase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1.7 M malic acid, 10 mM magnesium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.75→27.16 Å / Num. all: 35170 / Num. obs: 35169 / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 21.7
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 5.2 / Rsym value: 0.508 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceGUIdata collection
CCP4model building
REFMAC5.5.0109refinement
iMOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XUZ

1xuz


Resolution: 1.75→27.16 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.451 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 3541 10.1 %RANDOM
Rwork0.16132 ---
obs0.16491 31594 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.119 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 19 355 3066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222912
X-RAY DIFFRACTIONr_bond_other_d0.0010.021973
X-RAY DIFFRACTIONr_angle_refined_deg1.111.9823948
X-RAY DIFFRACTIONr_angle_other_deg0.8134868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4495380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5225.476126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5515526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0221512
X-RAY DIFFRACTIONr_chiral_restr0.0620.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213326
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02541
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_it0.4091.51834
X-RAY DIFFRACTIONr_mcbond_other0.0991.5748
X-RAY DIFFRACTIONr_mcangle_it0.80222968
X-RAY DIFFRACTIONr_scbond_it1.4931078
X-RAY DIFFRACTIONr_scangle_it2.5174.5980
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 246 -
Rwork0.216 2296 -
obs--99.96 %
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)
10.1780.04290.17650.72180.07360.1934-0.0031-0.0124-0.0006-0.0574-0.0061-0.10910.00580.01670.00910.02460.00150.01230.04780.00070.056101.3983-17.476249.6795
20.1559-0.1724-0.06820.44830.03210.0392-0.0168-0.00890.0156-0.00840.0026-0.03890.00180.00160.01430.03830.0011-0.00060.05660.00140.045398.8446-14.276154.6721
30.908-0.4495-1.17941.03530.86651.41110.1222-0.0606-0.01510.029-0.0921-0.0133-0.07870.0285-0.03010.0556-0.01720.01980.0441-0.02330.034774.810740.759866.5817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 79
2X-RAY DIFFRACTION2A80 - 282
3X-RAY DIFFRACTION3A283 - 349

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