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- PDB-7m15: crystal structure of cj1430 in the presence of GDP-D-glycero-L-gl... -

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Basic information

Entry
Database: PDB / ID: 7m15
Titlecrystal structure of cj1430 in the presence of GDP-D-glycero-L-gluco-heptose, a GDP-D-glycero-4-keto-D-lyxo-heptose-3,5-epimerase from campylobacter jejuni
ComponentsGDP-D-glycero-L-gluco-heptose
KeywordsISOMERASE / 3 / 5-epimerase / 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 / Chem-YO7 / 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: 1.85 Å
AuthorsGirardi, N.M. / Thoden, J.B. / 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)GM122825 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134643 United States
Robert A. Welch FoundationA-840 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.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _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 1.2Jun 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: GDP-D-glycero-L-gluco-heptose
B: GDP-D-glycero-L-gluco-heptose
C: GDP-D-glycero-L-gluco-heptose
D: GDP-D-glycero-L-gluco-heptose
E: GDP-D-glycero-L-gluco-heptose
F: GDP-D-glycero-L-gluco-heptose
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,31417
Polymers128,1926
Non-polymers4,12311
Water14,646813
1
A: GDP-D-glycero-L-gluco-heptose
B: GDP-D-glycero-L-gluco-heptose
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0635
Polymers42,7312
Non-polymers1,3333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-15 kcal/mol
Surface area15750 Å2
MethodPISA
2
C: GDP-D-glycero-L-gluco-heptose
D: GDP-D-glycero-L-gluco-heptose
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0635
Polymers42,7312
Non-polymers1,3333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-11 kcal/mol
Surface area15890 Å2
MethodPISA
3
E: GDP-D-glycero-L-gluco-heptose
F: GDP-D-glycero-L-gluco-heptose
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1887
Polymers42,7312
Non-polymers1,4575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-12 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.409, 81.569, 109.453
Angle α, β, γ (deg.)90.000, 94.380, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
GDP-D-glycero-L-gluco-heptose


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-YO7 / [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl dihydrogen diphosphate (non-preferred name)


Mass: 635.367 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H27N5O17P2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 813 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22-27% PEG-5000, 100 mM MOPS, 10 mM GDP-D-glycero-L-gluco-heptose

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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: Sep 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 99769 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rsym value: 0.083 / Net I/σ(I): 10.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 13932 / Rsym value: 0.389 / % possible all: 93.9

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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: 7m14

7m14


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.301 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 5212 5.2 %RANDOM
Rwork0.1901 ---
obs0.1924 94557 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.34 Å2 / Biso mean: 16.551 Å2 / Biso min: 2.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20.06 Å2
2--1.11 Å20 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8859 0 266 813 9938
Biso mean--13.04 22.1 -
Num. residues----1075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139396
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178437
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.68812798
X-RAY DIFFRACTIONr_angle_other_deg1.2781.59919632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.71251071
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22523.074475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.361151556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9051536
X-RAY DIFFRACTIONr_chiral_restr0.0720.21237
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021980
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 375 -
Rwork0.352 6621 -
all-6996 -
obs--93.4 %

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