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- PDB-1wlt: Crystal Structure of dTDP-4-dehydrorhamnose 3,5-epimerase homolog... -

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Basic information

Entry
Database: PDB / ID: 1wlt
TitleCrystal Structure of dTDP-4-dehydrorhamnose 3,5-epimerase homologue from Sulfolobus tokodaii
Components176aa long hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
KeywordsISOMERASE / jelly roll-like topology / flattened barrel
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 speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWatanabe, N. / Sakai, N. / Zilian, Z. / Kawarabayasi, Y. / Tanaka, I.
CitationJournal: to be published
Title: Crystal Structure of dTDP-4-dehydrorhamnose 3,5-epimerase homologue
Authors: Watanabe, N. / Sakai, N. / Zilian, Z. / Kawarabayasi, Y. / Tanaka, I.
History
DepositionJun 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 176aa long hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
B: 176aa long hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase


Theoretical massNumber of molelcules
Total (without water)45,3542
Polymers45,3542
Non-polymers00
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-15 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.147, 73.145, 126.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

#1: Protein 176aa long hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3 / 5-epimerase homologue


Mass: 22677.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: pET23q / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q96Z62, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.5 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% PEG 3350, 0.1M Sodium cacodylate buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 2, 2004 / Details: MONOCHROMETER
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. all: 35811 / Num. obs: 35811 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 24.5 Å2 / Rsym value: 0.06 / Net I/σ(I): 15.5
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 6.43 / Num. unique all: 3486 / Rsym value: 0.379 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ADSCdata collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DZR

1dzr


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.349 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 1759 5 %RANDOM
Rwork0.19705 ---
obs0.19957 33411 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.019 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2---0.87 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 0 272 3187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0223001
X-RAY DIFFRACTIONr_bond_other_d0.0020.022723
X-RAY DIFFRACTIONr_angle_refined_deg2.1371.9544054
X-RAY DIFFRACTIONr_angle_other_deg1.01136373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9145350
X-RAY DIFFRACTIONr_chiral_restr0.1470.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023258
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02632
X-RAY DIFFRACTIONr_nbd_refined0.1940.2544
X-RAY DIFFRACTIONr_nbd_other0.260.23231
X-RAY DIFFRACTIONr_nbtor_other0.0940.21752
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.310.25
X-RAY DIFFRACTIONr_mcbond_it1.3921.51769
X-RAY DIFFRACTIONr_mcangle_it2.31222901
X-RAY DIFFRACTIONr_scbond_it3.48831232
X-RAY DIFFRACTIONr_scangle_it5.3274.51153
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.299 113
Rwork0.215 2413
obs-2526

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