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- PDB-1xuz: Crystal structure analysis of sialic acid synthase (NeuB)from Nei... -

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Basic information

Entry
Database: PDB / ID: 1xuz
TitleCrystal structure analysis of sialic acid synthase (NeuB)from Neisseria meningitidis, bound to Mn2+, Phosphoenolpyruvate, and N-acetyl mannosaminitol
Componentspolysialic acid capsule biosynthesis protein SiaC
KeywordsBIOSYNTHETIC PROTEIN / TIM barrel / Antifreeze-like domain / Domain-swapped dimer
Function / homology
Function and homology information


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
5-DEOXY-5-{[(1S)-1-HYDROXYETHYL]AMINO}-D-GLUCITOL / : / PHOSPHOENOLPYRUVATE / Capsule biosynthesis protein
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.2 Å
AuthorsGunawan, J. / Simard, D. / Gilbert, M. / Lovering, A.L. / Wakarchuk, W.W. / Tanner, M.E. / Strynadka, N.C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural and mechanistic analysis of sialic acid synthase NeuB from Neisseria meningitidis in complex with Mn2+, phosphoenolpyruvate, and N-acetylmannosaminitol.
Authors: Gunawan, J. / Simard, D. / Gilbert, M. / Lovering, A.L. / Wakarchuk, W.W. / Tanner, M.E. / Strynadka, N.C.
History
DepositionOct 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,8444
Polymers38,3961
Non-polymers4483
Water4,594255
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)77,6888
Polymers76,7912
Non-polymers8966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,-y,z1
Buried area9440 Å2
ΔGint-55 kcal/mol
Surface area25660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.531, 75.654, 77.866
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a domain-swapped dimer generated from the monomer in the asymmetric unit by the operations: -x, -y, z; 1/2-x, 1/2+y, -z; 1/2+x, 1/2-y, -z

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Components

#1: Protein polysialic acid capsule biosynthesis protein SiaC / Sialic Acid Synthase / NeuB


Mass: 38395.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: neuB / Plasmid: pCWori+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q57265
#2: Sugar ChemComp-MMN / 5-DEOXY-5-{[(1S)-1-HYDROXYETHYL]AMINO}-D-GLUCITOL / N-ACETYLMANNOSAMINITOL


Type: saccharide / Mass: 225.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H19NO6
#3: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Crystal Buffer Exchange, Malic Acid, Sodium Phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 29, 2004 / Details: mirrors
RadiationMonochromator: CuK alpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 17331 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 9.2 / Num. unique all: 2395 / Rsym value: 0.078 / % possible all: 95

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→30 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 1725 -random
Rwork0.1863 ---
obs0.1863 17313 95.4 %-
all-18148 --
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 26 255 2962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.2→2.24 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection
Rfree0.3012 46
Rwork0.2118 -
obs-369

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