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- PDB-2b9u: Crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase from su... -

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Basic information

Entry
Database: PDB / ID: 2b9u
TitleCrystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase from sulfolobus tokodaii
Componentshypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
KeywordsISOMERASE / BETA CLASS / 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 / 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: 2.07 Å
AuthorsRajakannan, V. / Kondo, K. / Mizushima, T. / Suzuki, A. / Yamane, T.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase from sulfolobus tokodaii
Authors: Rajakannan, V. / Kondo, K. / Mizushima, T. / Suzuki, A. / Yamane, T.
History
DepositionOct 13, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_close_contact
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
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: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
C: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
D: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
B: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
E: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
F: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
G: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
H: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
I: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
J: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
K: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
L: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase


Theoretical massNumber of molelcules
Total (without water)246,06912
Polymers246,06912
Non-polymers00
Water31,4721747
1
A: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
C: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase


Theoretical massNumber of molelcules
Total (without water)41,0112
Polymers41,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-15 kcal/mol
Surface area15690 Å2
MethodPISA
2
D: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
B: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase


Theoretical massNumber of molelcules
Total (without water)41,0112
Polymers41,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-15 kcal/mol
Surface area15510 Å2
MethodPISA
3
E: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
F: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase


Theoretical massNumber of molelcules
Total (without water)41,0112
Polymers41,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-14 kcal/mol
Surface area15630 Å2
MethodPISA
4
G: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
H: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase


Theoretical massNumber of molelcules
Total (without water)41,0112
Polymers41,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-14 kcal/mol
Surface area15550 Å2
MethodPISA
5
I: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
J: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase


Theoretical massNumber of molelcules
Total (without water)41,0112
Polymers41,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-13 kcal/mol
Surface area15620 Å2
MethodPISA
6
K: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase
L: hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase


Theoretical massNumber of molelcules
Total (without water)41,0112
Polymers41,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-11 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.788, 229.495, 74.583
Angle α, β, γ (deg.)90.00, 96.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase


Mass: 20505.736 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: str. 7 / Gene: ARCHAEA / Production host: Escherichia coli (E. coli)
References: UniProt: Q96Z62, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1747 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 2.0M Na/K pH 7.1, 34% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Sep 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 150049 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 %
Reflection shellResolution: 2.07→2.14 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DZR

1dzr


Resolution: 2.07→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.438 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.25 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 14935 10 %RANDOM
Rwork0.20313 ---
all0.225 149849 --
obs0.20854 134914 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.442 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å2-0.6 Å2
2---1.09 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.07→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17364 0 0 1747 19111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02217880
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.96224168
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11252100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85323.714840
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.838153180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3831596
X-RAY DIFFRACTIONr_chiral_restr0.0950.22532
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213632
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.28388
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.211952
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2940.21753
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.2152
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.266
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0151.510980
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.203217352
X-RAY DIFFRACTIONr_scbond_it1.97237918
X-RAY DIFFRACTIONr_scangle_it2.8964.56816
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.071→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 1047 -
Rwork0.237 9575 -
obs--96.65 %

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