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- PDB-3m2p: The crystal structure of UDP-N-acetylglucosamine 4-epimerase from... -

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Basic information

Entry
Database: PDB / ID: 3m2p
TitleThe crystal structure of UDP-N-acetylglucosamine 4-epimerase from Bacillus cereus
ComponentsUDP-N-acetylglucosamine 4-epimerase
KeywordsISOMERASE / SGXNY / 11155j / UDP / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


UDP-N-acetylglucosamine 4-epimerase / UDP-N-acetylglucosamine 4-epimerase activity / nucleotide binding
Similarity search - Function
NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine 4-epimerase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of UDP-N-acetylglucosamine 4-epimerase from Bacillus cereus
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionMar 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine 4-epimerase
B: UDP-N-acetylglucosamine 4-epimerase
C: UDP-N-acetylglucosamine 4-epimerase
D: UDP-N-acetylglucosamine 4-epimerase
E: UDP-N-acetylglucosamine 4-epimerase
F: UDP-N-acetylglucosamine 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,1427
Polymers211,7376
Non-polymers4041
Water2,054114
1
A: UDP-N-acetylglucosamine 4-epimerase
B: UDP-N-acetylglucosamine 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9833
Polymers70,5792
Non-polymers4041
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-22 kcal/mol
Surface area24010 Å2
MethodPISA
2
C: UDP-N-acetylglucosamine 4-epimerase
F: UDP-N-acetylglucosamine 4-epimerase


Theoretical massNumber of molelcules
Total (without water)70,5792
Polymers70,5792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-18 kcal/mol
Surface area24220 Å2
MethodPISA
3
D: UDP-N-acetylglucosamine 4-epimerase
E: UDP-N-acetylglucosamine 4-epimerase


Theoretical massNumber of molelcules
Total (without water)70,5792
Polymers70,5792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-15 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.116, 149.725, 166.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Details2

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Components

#1: Protein
UDP-N-acetylglucosamine 4-epimerase


Mass: 35289.578 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC_5271 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) Codon+ril Stratagene
References: UniProt: Q814Z6, UDP-N-acetylglucosamine 4-epimerase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4 M Sodium malonate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.95→111.28 Å / Num. obs: 55533 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 64.6 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 13.5
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.95→72.701 Å / SU ML: 0.45 / Isotropic thermal model: Isotropic / σ(F): 1.76 / Phase error: 25.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2757 2822 5.09 %
Rwork0.2116 --
obs0.2149 55442 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.69 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso mean: 49.31 Å2
Baniso -1Baniso -2Baniso -3
1-16.8812 Å2-0 Å2-0 Å2
2---7.5692 Å20 Å2
3----9.312 Å2
Refinement stepCycle: LAST / Resolution: 2.95→72.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12928 0 25 114 13067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713198
X-RAY DIFFRACTIONf_angle_d1.05517843
X-RAY DIFFRACTIONf_dihedral_angle_d19.1124667
X-RAY DIFFRACTIONf_chiral_restr0.071983
X-RAY DIFFRACTIONf_plane_restr0.0042302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.00080.31981480.24242593X-RAY DIFFRACTION100
3.0008-3.05540.29471360.24022602X-RAY DIFFRACTION100
3.0554-3.11420.31551610.23162573X-RAY DIFFRACTION100
3.1142-3.17770.27541420.23432588X-RAY DIFFRACTION100
3.1777-3.24680.32181150.23332639X-RAY DIFFRACTION100
3.2468-3.32240.30841430.22662587X-RAY DIFFRACTION100
3.3224-3.40550.27491390.20522591X-RAY DIFFRACTION100
3.4055-3.49750.23411360.18582618X-RAY DIFFRACTION100
3.4975-3.60040.24951380.18232593X-RAY DIFFRACTION100
3.6004-3.71670.25871490.19362624X-RAY DIFFRACTION100
3.7167-3.84950.27381280.19082619X-RAY DIFFRACTION100
3.8495-4.00360.24141490.18482616X-RAY DIFFRACTION100
4.0036-4.18580.24181320.19022621X-RAY DIFFRACTION100
4.1858-4.40640.25411410.18422625X-RAY DIFFRACTION100
4.4064-4.68250.26351320.18582652X-RAY DIFFRACTION100
4.6825-5.04390.26131220.19222654X-RAY DIFFRACTION100
5.0439-5.55140.25281570.1982643X-RAY DIFFRACTION100
5.5514-6.35430.27611500.22862669X-RAY DIFFRACTION100
6.3543-8.00410.26641450.2242701X-RAY DIFFRACTION100
8.0041-72.72320.2711590.23322812X-RAY DIFFRACTION100

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