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- PDB-5buv: X-ray structure of WbcA from Yersinia enterocolitica -

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Basic information

Entry
Database: PDB / ID: 5buv
TitleX-ray structure of WbcA from Yersinia enterocolitica
ComponentsPutative epimerase
KeywordsISOMERASE / lipopolysaccharide
Function / homology
Function and homology information


: / dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
6-AMINOPYRIMIDIN-2(1H)-ONE / PHOSPHATE ION / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesYersinia enterocolitica subsp. enterocolitica 8081 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHolden, H.M. / Salinger, A.J. / Brown, H.A. / Thoden, J.B.
CitationJournal: Protein Sci. / Year: 2015
Title: Biochemical studies on WbcA, a sugar epimerase from Yersinia enterocolitica.
Authors: Salinger, A.J. / Brown, H.A. / Thoden, J.B. / Holden, H.M.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Nov 15, 2017Group: Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._citation.journal_id_CSD / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative epimerase
B: Putative epimerase
C: Putative epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,44911
Polymers61,6903
Non-polymers7598
Water7,206400
1
A: Putative epimerase
C: Putative epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5857
Polymers41,1262
Non-polymers4585
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-27 kcal/mol
Surface area15330 Å2
MethodPISA
2
B: Putative epimerase
hetero molecules

B: Putative epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7298
Polymers41,1262
Non-polymers6026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4680 Å2
ΔGint-37 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.160, 42.678, 150.463
Angle α, β, γ (deg.)90.00, 90.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative epimerase / WbcA


Mass: 20563.232 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica subsp. enterocolitica 8081 (bacteria)
Strain: NCTC 13174 / 8081 / Gene: wbcA, YE3085 / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta2(DE3) / References: UniProt: A1JNA0
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE


Mass: 111.102 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5N3O
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14-18% PEG5000-OMe, 5 mM CPD-6-deoxygulose, 2% glycerol, 100 mM MOPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 50180 / Num. obs: 50180 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Redundancy: 2.5 % / Rsym value: 0.082 / Net I/σ(I): 6.9
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hn0

4hn0


Resolution: 1.75→27.36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.442 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24795 2541 5.1 %RANDOM
Rwork0.19229 ---
obs0.19513 47639 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.778 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.03 Å2
2--0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.75→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4253 0 45 400 4698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194449
X-RAY DIFFRACTIONr_bond_other_d00.024073
X-RAY DIFFRACTIONr_angle_refined_deg1.9981.9416024
X-RAY DIFFRACTIONr_angle_other_deg0.80839399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1825536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48424.156231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59915754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3431524
X-RAY DIFFRACTIONr_chiral_restr0.1210.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215076
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021122
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.328 191 -
Rwork0.298 3422 -
obs--95.3 %

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