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- PDB-2uvk: Structure of YjhT -

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Basic information

Entry
Database: PDB / ID: 2uvk
TitleStructure of YjhT
ComponentsYJHT
KeywordsUNKNOWN FUNCTION / HYPOTHETICAL PROTEIN / SIALIC ACID METABOLISM / KELCH REPEAT / BETA-PROPELLER
Function / homologyN-acetylneuraminate epimerase / Mutatrotase, YjhT-like / racemase and epimerase activity, acting on carbohydrates and derivatives / N-acetylneuraminate catabolic process / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Kelch-type beta propeller / outer membrane-bounded periplasmic space / protein homodimerization activity / N-acetylneuraminate epimerase
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMuller, A. / Severi, E. / Wilson, K.S. / Thomas, G.H.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Sialic Acid Mutarotation is Catalyzed by the Escherichia Coli Beta-Propeller Protein Yjht.
Authors: Severi, E. / Muller, A. / Potts, J.R. / Leech, A. / Williamson, D. / Wilson, K.S. / Thomas, G.H.
History
DepositionMar 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YJHT
B: YJHT


Theoretical massNumber of molelcules
Total (without water)77,7452
Polymers77,7452
Non-polymers00
Water13,133729
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-9.48 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.758, 105.659, 74.222
Angle α, β, γ (deg.)90.00, 99.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein YJHT


Mass: 38872.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P39371
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 7.5
Details: 150 NL OF SEMET-SUBSTITUTED YJHT AND 150 NL OF 200 MM SODIUM MALONATE, 0.1M BIS TRIS PROPANE PH 7.5 AND 20% W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→52.85 Å / Num. obs: 107873 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.1
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.9 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXCDphasing
SHELXEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→73.13 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.403 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 5376 5 %RANDOM
Rwork0.18 ---
obs0.182 102206 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0.09 Å2
2--0.52 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→73.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5167 0 0 729 5896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0215462
X-RAY DIFFRACTIONr_bond_other_d0.0010.023500
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9187455
X-RAY DIFFRACTIONr_angle_other_deg0.80838547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97625.083240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68315776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.971158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021161
X-RAY DIFFRACTIONr_nbd_refined0.1940.2962
X-RAY DIFFRACTIONr_nbd_other0.190.23533
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22716
X-RAY DIFFRACTIONr_nbtor_other0.0840.22754
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2515
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.221
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: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 408 -
Rwork0.22 7508 -
obs--98.49 %

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