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- PDB-3dzc: 2.35 Angstrom resolution structure of WecB (VC0917), a UDP-N-acet... -

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Basic information

Entry
Database: PDB / ID: 3dzc
Title2.35 Angstrom resolution structure of WecB (VC0917), a UDP-N-acetylglucosamine 2-epimerase from Vibrio cholerae.
ComponentsUDP-N-acetylglucosamine 2-epimerase
KeywordsISOMERASE / UDP-N-acetylglucosamine 2-epimerase / Structural Genomics / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase activity / metal ion binding
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
UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Kwon, K. / Hasseman, J. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.35 Angstrom resolution structure of WecB (VC0917), a UDP-N-acetylglucosamine 2-epimerase from Vibrio cholerae.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Kwon, K. / Hasseman, J. / Peterson, S.N. / Anderson, W.F.
History
DepositionJul 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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: UDP-N-acetylglucosamine 2-epimerase
B: UDP-N-acetylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7996
Polymers87,6482
Non-polymers1514
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-51 kcal/mol
Surface area31240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.391, 88.127, 132.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UDP-N-acetylglucosamine 2-epimerase


Mass: 43823.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 / Gene: VC_0917 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: Q9KTI5, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1:1 V/V. Protein solution: 7.9mG/mL of protein, 0.5M NaCl, 10mM TRIS-HCL, 10 mM UDP. Reservoir solution (PACT, #23): 0.2M Calcium chloride, 0.1M MES, 20% w/v PEG 6000, pH 6.0, Vapor ...Details: 1:1 V/V. Protein solution: 7.9mG/mL of protein, 0.5M NaCl, 10mM TRIS-HCL, 10 mM UDP. Reservoir solution (PACT, #23): 0.2M Calcium chloride, 0.1M MES, 20% w/v PEG 6000, pH 6.0, Vapor Diffusion, sitting drop, Temp. 295K., VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2008 / Details: beryllium lenses
RadiationMonochromator: single diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 40522 / Num. obs: 40522 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 47.9 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 17.9
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3962 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-IceMaxdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F6D

1f6d


Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.148 / SU ML: 0.15
Isotropic thermal model: Individual Isotropic thermal refinement
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.309 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23376 2012 5 %RANDOM
Rwork0.17238 ---
all0.17542 38263 --
obs0.17542 38263 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.448 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å20 Å20 Å2
2--1.02 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 4 488 6264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226255
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9698556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3515818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55925.524286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.762151100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3031531
X-RAY DIFFRACTIONr_chiral_restr0.110.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024841
X-RAY DIFFRACTIONr_nbd_refined0.2120.22954
X-RAY DIFFRACTIONr_nbtor_refined0.30.24386
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2477
X-RAY DIFFRACTIONr_metal_ion_refined0.060.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.216
X-RAY DIFFRACTIONr_mcbond_it1.2781.54113
X-RAY DIFFRACTIONr_mcangle_it2.09826468
X-RAY DIFFRACTIONr_scbond_it3.10932397
X-RAY DIFFRACTIONr_scangle_it4.7464.52088
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 135 -
Rwork0.194 2786 -
obs-2786 99.49 %

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