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- PDB-8db5: Crystal structure of the GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-... -

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Basic information

Entry
Database: PDB / ID: 8db5
TitleCrystal structure of the GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase from Campylobacter jejuni, serotype HS:15
ComponentsGDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
KeywordsISOMERASE / 3 / 5-epimerase / Campylobacter / capsular polysaccharide
Function / homologydTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / cytosol / GUANOSINE-5'-DIPHOSPHATE / dTDP-4-dehydrorhamnose 3,5-epimerase
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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)GM139428 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)GM134643 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 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 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-3,5-epimerase
B: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
C: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
D: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
E: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
F: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
G: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
H: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,10023
Polymers171,3068
Non-polymers3,79415
Water18,8261045
1
A: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
B: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7846
Polymers42,8272
Non-polymers9574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-48 kcal/mol
Surface area15090 Å2
MethodPISA
2
C: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
D: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7485
Polymers42,8272
Non-polymers9223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-36 kcal/mol
Surface area15000 Å2
MethodPISA
3
E: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
F: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7846
Polymers42,8272
Non-polymers9574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-47 kcal/mol
Surface area15060 Å2
MethodPISA
4
G: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
H: GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7846
Polymers42,8272
Non-polymers9574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-47 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.549, 154.525, 120.506
Angle α, β, γ (deg.)90.000, 91.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase


Mass: 21413.299 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: serotype HS:15 / Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: HS58.11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2
References: UniProt: A0A0S2CFK0, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1045 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Enzyme pre-incubated with 5 mM GDP; precipitant: 26-28% PEG8000, 100 mM MES

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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: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 118325 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rpim(I) all: 0.081 / Net I/σ(I): 9.3
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8051 / Rsym value: 0.389 / % possible all: 96.9

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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: 1.9→36.81 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.899 / SU B: 4.509 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 5910 5 %RANDOM
Rwork0.1889 ---
obs0.1913 112415 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.27 Å2 / Biso mean: 14.664 Å2 / Biso min: 3.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.9→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11618 0 231 1045 12894
Biso mean--20.56 21.46 -
Num. residues----1412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01312243
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710958
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.67116712
X-RAY DIFFRACTIONr_angle_other_deg1.2731.58725501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.53251421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77823.349639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.057152021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3941548
X-RAY DIFFRACTIONr_chiral_restr0.0750.21581
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213387
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022609
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 474 -
Rwork0.304 8051 -
all-8525 -
obs--96.85 %

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