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- PDB-7us5: X-ray crystal structure of GDP-D-glycero-D-manno-heptose 4,6-Dehy... -

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Basic information

Entry
Database: PDB / ID: 7us5
TitleX-ray crystal structure of GDP-D-glycero-D-manno-heptose 4,6-Dehydratase from Campylobacter jejuni
ComponentsGDP-D-GLYCERO-D-MANNO-HEPTOSE 4,6-DEHYDRATASE
KeywordsOXIDOREDUCTASE / dehydratase / capsular polysaccharide
Function / homologyGDP-mannose 4,6 dehydratase / NAD(P)-binding domain / NAD(P)-binding domain superfamily / GUANOSINE-5'-DIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / GDP-mannose 4,6-dehydratase
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsThoden, J.B. / 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)GM 122825 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 134643 United States
CitationJournal: Biochemistry / Year: 2022
Title: Reaction Mechanism and Three-Dimensional Structure of GDP-d-glycero-alpha-d-manno-heptose 4,6-Dehydratase from Campylobacter jejuni.
Authors: Xiang, D.F. / Thoden, J.B. / Ghosh, M.K. / Holden, H.M. / Raushel, F.M.
History
DepositionApr 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: GDP-D-GLYCERO-D-MANNO-HEPTOSE 4,6-DEHYDRATASE
B: GDP-D-GLYCERO-D-MANNO-HEPTOSE 4,6-DEHYDRATASE
C: GDP-D-GLYCERO-D-MANNO-HEPTOSE 4,6-DEHYDRATASE
D: GDP-D-GLYCERO-D-MANNO-HEPTOSE 4,6-DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,23218
Polymers166,4334
Non-polymers4,79914
Water16,880937
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24070 Å2
ΔGint-100 kcal/mol
Surface area42440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.673, 182.950, 75.397
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-606-

HOH

21A-636-

HOH

31A-705-

HOH

41B-510-

HOH

51B-574-

HOH

61B-674-

HOH

71B-731-

HOH

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Components

#1: Protein
GDP-D-GLYCERO-D-MANNO-HEPTOSE 4,6-DEHYDRATASE / GDP-mannose 4 / 6-dehydratase / GDP-D-GLYCERO-D-MANNO-HEPTOSE 4 / 6-DEHYDRATASE / SDR FAMILY


Mass: 41608.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: dmhA, BBR99_05330, F1P94_08755, HS23.12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q5M6Q7
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 937 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein incubated with 5 mM GDP. Precipitant used was 6-10% PEG-8000, 200 mM tetramethylammonium chloride, 100 mM HEPPS (pH 8)

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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: Jun 3, 2021
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: 91209 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.091 / Net I/σ(I): 11.2
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3 / Num. unique obs: 11616 / Rsym value: 0.37 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pk3

2pk3


Resolution: 2.1→36.97 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.424 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 4572 5 %RANDOM
Rwork0.169 ---
obs0.1715 86637 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.4 Å2 / Biso mean: 18.792 Å2 / Biso min: 3.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.1→36.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11013 0 312 939 12264
Biso mean--15.58 22 -
Num. residues----1373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01311658
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710676
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.66415807
X-RAY DIFFRACTIONr_angle_other_deg1.2991.58424813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.68851399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58522.24643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.762152046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9091584
X-RAY DIFFRACTIONr_chiral_restr0.0740.21550
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212957
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022495
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 349 -
Rwork0.272 6275 -
all-6624 -
obs--98.62 %

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