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- PDB-4fkz: Crystal structure of Bacillus subtilis UDP-GlcNAc 2-epimerase in ... -

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Basic information

Entry
Database: PDB / ID: 4fkz
TitleCrystal structure of Bacillus subtilis UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP
ComponentsUDP-N-acetylglucosamine 2-epimerase
KeywordsBIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase activity / teichoic acid biosynthetic process / cell wall organization / cytoplasm
Similarity search - Function
UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine 2-epimerase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsYang, C.S. / Chen, S.C. / Kuan, S.M. / Chen, Y.R. / Liu, Y.H. / Chen, Y.
CitationJournal: To be Published
Title: Crystal structure of Bacillus subtilis UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc and UDP
Authors: Yang, C.S. / Chen, S.C. / Kuan, S.M. / Chen, Y.R. / Liu, Y.H. / Chen, Y.
History
DepositionJun 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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 / _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 2-epimerase
B: UDP-N-acetylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5526
Polymers87,5292
Non-polymers2,0234
Water18,1591008
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-61 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.289, 209.338, 46.810
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 UDP-N-acetylglucosamine 2-epimerase / UDP-GlcNAc-2-epimerase


Mass: 43764.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU35660, mnaA / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P39131, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing)
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1008 / 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: 2.55 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 70% MPD, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 3, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. all: 101913 / Num. obs: 99875 / % possible obs: 98 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.53
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.07 / Num. unique all: 9869 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BEO

3beo


Resolution: 1.69→32.29 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.776 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19875 5006 5 %RANDOM
Rwork0.17033 ---
all0.1718 101913 --
obs0.1718 94854 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.704 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.69→32.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6017 0 128 1008 7153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026276
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9898520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46624.597298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.652151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5741536
X-RAY DIFFRACTIONr_chiral_restr0.0820.2959
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214712
LS refinement shellResolution: 1.69→1.732 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 328 -
Rwork0.265 6505 -
obs-6505 96.78 %

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