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- PDB-7m14: x-ray structure of cj1430 in the presence of GDP, a GDP-D-glycero... -

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Basic information

Entry
Database: PDB / ID: 7m14
Titlex-ray structure of cj1430 in the presence of GDP, a GDP-D-glycero-4-keto-D-lyxo-heptose-3,5-epimerase from campylobacter jejuni
ComponentsThymidine diphospho-4-keto-rhamnose 3,5-epimerase
KeywordsISOMERASE / 3 / 5-epimerase / capsular polycassharide
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 subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGirardi, N.M. / Thoden, J.B. / Raushel, F.M. / Holden, H.M.
Funding support United States, 2items
OrganizationGrant numberCountry
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: 2021
Title: Biosynthesis of d- glycero -l- gluco -Heptose in the Capsular Polysaccharides of Campylobacter jejuni .
Authors: Huddleston, J.P. / Anderson, T.K. / Girardi, N.M. / Thoden, J.B. / Taylor, Z. / Holden, H.M. / Raushel, F.M.
History
DepositionMar 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: 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
Revision 1.2Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
B: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
C: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
D: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
E: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
F: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,99815
Polymers128,1926
Non-polymers2,8069
Water11,620645
1
A: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
B: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6405
Polymers42,7312
Non-polymers9093
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-31 kcal/mol
Surface area15460 Å2
MethodPISA
2
C: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
D: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6795
Polymers42,7312
Non-polymers9483
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-21 kcal/mol
Surface area15090 Å2
MethodPISA
3
E: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
F: Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6795
Polymers42,7312
Non-polymers9483
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-24 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.286, 83.709, 110.044
Angle α, β, γ (deg.)90.000, 94.740, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-371-

HOH

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Components

#1: Protein
Thymidine diphospho-4-keto-rhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3 / 5-epimerase / dTDP-4-keto-6-deoxyglucose 3 / dTDP-6-deoxy-D-xylo-4-hexulose 3


Mass: 21365.320 Da / Num. of mol.: 6 / Mutation: K128A, E129A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: rfbC, Cj1430c / Production host: Escherichia coli (E. coli)
References: UniProt: Q0P8I4, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 22-27% PEG-5000, 100 mM MOPS, 10 mM GDP

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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: Aug 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 69127 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.088 / Net I/σ(I): 9.7
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8583 / Rsym value: 0.39 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ryk

3ryk


Resolution: 2.1→27.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.744 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 3408 4.9 %RANDOM
Rwork0.2018 ---
obs0.2049 65719 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.69 Å2 / Biso mean: 26.749 Å2 / Biso min: 5.08 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å2-0.12 Å2
2--1.63 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 2.1→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8738 0 177 645 9560
Biso mean--29.99 27.56 -
Num. residues----1064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139203
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178314
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.67412533
X-RAY DIFFRACTIONr_angle_other_deg1.2221.59119317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.56251065
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65623.22469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.069151536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.341535
X-RAY DIFFRACTIONr_chiral_restr0.0690.21194
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021973
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 239 -
Rwork0.317 4579 -
all-4818 -
obs--92.26 %

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