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- PDB-1epz: CRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULOASE 3,5-EPIMERAS... -

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Basic information

Entry
Database: PDB / ID: 1epz
TitleCRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULOASE 3,5-EPIMERASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM WITH BOUND LIGAND.
ComponentsDTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE
KeywordsISOMERASE / racemase / dTDP-4-dehydrorhamnose epimerase
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process
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
THYMIDINE-5'-DIPHOSPHATE / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsChristendat, D. / Saridakis, V. / Bochkarev, A. / Pai, E.F. / Arrowsmith, C. / Edwards, A.M.
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 30, 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: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,1052
Polymers21,7021
Non-polymers4021
Water2,144119
1
A: DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)44,2094
Polymers43,4052
Non-polymers8042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4890 Å2
ΔGint-25 kcal/mol
Surface area15240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.156, 53.486, 51.462
Angle α, β, γ (deg.)90.00, 97.22, 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: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. all: 63707 / Num. obs: 17671 / % possible obs: 95 % / Observed criterion σ(F): 4862 / Observed criterion σ(I): 206 / Redundancy: 4 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 24
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4 % / Rmerge(I) obs: 0.321 / Num. unique all: 1708 / % possible all: 92
Reflection
*PLUS
% possible obs: 95.2 % / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 4

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.75→9.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 456278.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS 0.9 / Details: Simulated Annealing
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1702 9.9 %RANDOM
Rwork0.196 ---
obs0.196 17222 92.8 %-
all-63707 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.66 Å2 / ksol: 0.536 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20 Å2-0.64 Å2
2--1.77 Å20 Å2
3----3.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 25 119 1662
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.921.5
X-RAY DIFFRACTIONc_mcangle_it1.522
X-RAY DIFFRACTIONc_scbond_it1.582
X-RAY DIFFRACTIONc_scangle_it2.452.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 246 9.5 %
Rwork0.243 2340 -
obs--83.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAMTDP.PARAM
X-RAY DIFFRACTION4TDP.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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