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- PDB-4zrm: Crystal Structure of UDP-Glucose 4-Epimerase (TM0509) from Hypert... -

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Basic information

Entry
Database: PDB / ID: 4zrm
TitleCrystal Structure of UDP-Glucose 4-Epimerase (TM0509) from Hyperthermophilic Eubacterium Thermotoga maritima
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / Thermotoga maritima / Hyperthermophiles / epimerization
Function / homology
Function and homology information


UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / UDP-glucose 4-epimerase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChoi, J.M. / Lee, D.W. / Lee, S.H.
CitationJournal: Arch.Biochem.Biophys. / Year: 2015
Title: The structural basis of substrate promiscuity in UDP-hexose 4-epimerase from the hyperthermophilic Eubacterium Thermotoga maritima.
Authors: Shin, S.M. / Choi, J.M. / di Luccio, E. / Lee, Y.J. / Lee, S.J. / Lee, S.J. / Lee, S.H. / Lee, D.W.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucose 4-epimerase
B: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0557
Polymers70,4522
Non-polymers1,6035
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-35 kcal/mol
Surface area24570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.542, 150.262, 60.606
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-glucose 4-epimerase / UDP-glucose 4-epimerase / putative / Uncharacterized protein


Mass: 35226.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0509, THEMA_02130, Tmari_0505 / Plasmid: pET28a(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WYX9, UDP-glucose 4-epimerase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 8% Tascimate pH 5.0, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2013
RadiationMonochromator: Si(111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 60368 / % possible obs: 99 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 29.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 8.3 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P5Y

2p5y


Resolution: 1.9→34.972 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1841 3055 5.06 %Random
Rwork0.157 ---
obs0.1584 59877 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→34.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4914 0 106 282 5302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075134
X-RAY DIFFRACTIONf_angle_d1.1496949
X-RAY DIFFRACTIONf_dihedral_angle_d14.6121924
X-RAY DIFFRACTIONf_chiral_restr0.079756
X-RAY DIFFRACTIONf_plane_restr0.005879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8872-1.91670.23861200.17142122X-RAY DIFFRACTION82
1.9167-1.94810.20621190.17182554X-RAY DIFFRACTION96
1.9481-1.98170.21641340.15772513X-RAY DIFFRACTION96
1.9817-2.01780.18731390.15632551X-RAY DIFFRACTION97
2.0178-2.05660.20831430.15132530X-RAY DIFFRACTION98
2.0566-2.09850.17271310.15172598X-RAY DIFFRACTION98
2.0985-2.14420.17451330.14942562X-RAY DIFFRACTION98
2.1442-2.1940.19761240.15042604X-RAY DIFFRACTION99
2.194-2.24890.18861550.15292599X-RAY DIFFRACTION99
2.2489-2.30970.15741480.15322600X-RAY DIFFRACTION99
2.3097-2.37760.19681310.16192636X-RAY DIFFRACTION100
2.3776-2.45440.20571580.16362619X-RAY DIFFRACTION100
2.4544-2.54210.2041290.16682650X-RAY DIFFRACTION100
2.5421-2.64380.22891430.16062637X-RAY DIFFRACTION100
2.6438-2.76410.18691320.16782674X-RAY DIFFRACTION100
2.7641-2.90980.20021390.17312630X-RAY DIFFRACTION100
2.9098-3.0920.19621360.16962657X-RAY DIFFRACTION100
3.092-3.33050.18651440.162684X-RAY DIFFRACTION100
3.3305-3.66540.16891320.15222686X-RAY DIFFRACTION100
3.6654-4.1950.14381510.14362681X-RAY DIFFRACTION100
4.195-5.28230.14821330.13872718X-RAY DIFFRACTION99
5.2823-34.97810.19641810.16752808X-RAY DIFFRACTION99

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