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- PDB-1ep0: HIGH RESOLUTION CRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULO... -

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Basic information

Entry
Database: PDB / ID: 1ep0
TitleHIGH RESOLUTION CRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
ComponentsDTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE
KeywordsISOMERASE / racemase / dTDP-4-dehydrorhamnose epimerase / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / polysaccharide 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
dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsChristendat, D. / Saridakis, V. / Bochkarev, A. / Pai, E.F. / Arrowsmith, C.H. / Edwards, A.M. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Crystal structure of dTDP-4-keto-6-deoxy-D-hexulose 3,5-epimerase from Methanobacterium thermoautotrophicum complexed with dTDP.
Authors: Christendat, D. / Saridakis, V. / Dharamsi, A. / Bochkarev, A. / Pai, E.F. / Arrowsmith, C.H. / Edwards, A.M.
History
DepositionMar 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE


Theoretical massNumber of molelcules
Total (without water)21,7021
Polymers21,7021
Non-polymers00
Water2,270126
1
A: DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE

A: DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE


Theoretical massNumber of molelcules
Total (without water)43,4052
Polymers43,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)67.720, 53.131, 51.667
Angle α, β, γ (deg.)90.00, 96.61, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer constructed from Chain A and one symmetry related molecule.

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Components

#1: Protein DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE / DTDP-4-DEHYDRORHAMNOSE 3 / 5-EPIMERASE


Mass: 21702.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Plasmid: PET15B / Production host: Escherichia coli (E. coli)
References: UniProt: O27818, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 10 % Polyethylene glycol 4K, 0.1 M Sodium Acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal
*PLUS
Density % sol: 46 %
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG40001reservoir
2100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.953733
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953733 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 180757 / Num. obs: 29180 / % possible obs: 99.7 % / Observed criterion σ(F): 5592 / Observed criterion σ(I): 150.7 / Redundancy: 8 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 37.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.105 / Num. unique all: 2877 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 99.5 % / Mean I/σ(I) obs: 9.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNS0.9refinement
RefinementResolution: 1.5→25.66 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 501863.81 / Data cutoff high rms absF: 501863.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS 0.9 / Details: Simulated Annealing
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2933 10.1 %RANDOM
Rwork0.183 ---
obs0.183 29020 99.2 %-
all-180757 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.1104 Å2 / ksol: 0.422673 e/Å3
Displacement parametersBiso mean: 13.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å2-0.19 Å2
2---0.22 Å20 Å2
3----1.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.05 Å-0.06 Å
Refinement stepCycle: LAST / Resolution: 1.5→25.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 0 126 1644
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_mcbond_it1.661.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it2.512
X-RAY DIFFRACTIONc_scangle_it3.762.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.197 474 10 %
Rwork0.17 4279 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24

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