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- PDB-8dcl: Crystal structure of the GDP-D-glycero-4-keto-D-lyxo-heptose-3-ep... -

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Basic information

Entry
Database: PDB / ID: 8dcl
TitleCrystal structure of the GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase from campylobacter jejuni, serotype HS:23/36
ComponentsGDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase
KeywordsISOMERASE / 3-epimerase / Campylobacter / capsular polysaccharide
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / 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 / RmlC-like jelly roll fold
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsThoden, J.B. / Ghosh, M.K. / Xiang, D.F. / Raushel, F.M. / Holden, H.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 139428 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122825 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 134643 United States
CitationJournal: Biochemistry / Year: 2022
Title: C3- and C3/C5-Epimerases Required for the Biosynthesis of the Capsular Polysaccharides from Campylobacter jejuni .
Authors: Ghosh, M.K. / Xiang, D.F. / Thoden, J.B. / Holden, H.M. / Raushel, F.M.
History
DepositionJun 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase
B: GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8709
Polymers43,7982
Non-polymers1,0737
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-43 kcal/mol
Surface area15220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.840, 44.766, 57.428
Angle α, β, γ (deg.)83.250, 79.350, 65.080
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase


Mass: 21898.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: serotype HS:23/36 / Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: BBR99_05345, F1P94_09915, HS23.15 / Variant: serotype HS:23/36 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q6EF58, dTDP-4-dehydrorhamnose 3,5-epimerase

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Non-polymers , 5 types, 411 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein incubated with 5 mM GDP; precipitant: 18-20% PEG3350, 200 mM potassium chloride, 100 mM HEPES, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 48120 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.049 / Net I/σ(I): 15.5
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 7423 / Rsym value: 0.258 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7M14

7m14


Resolution: 1.55→35.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.833 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 2448 5.1 %RANDOM
Rwork0.1649 ---
obs0.1667 45672 93.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.76 Å2 / Biso mean: 15.814 Å2 / Biso min: 6.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.55→35.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 64 406 3413
Biso mean--25.83 27.98 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133111
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172818
X-RAY DIFFRACTIONr_angle_refined_deg1.761.6734238
X-RAY DIFFRACTIONr_angle_other_deg1.5021.5926549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1365367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05323.025162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17415519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7411513
X-RAY DIFFRACTIONr_chiral_restr0.090.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023415
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02668
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 165 -
Rwork0.318 3015 -
all-3180 -
obs--83.18 %

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