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- PDB-7cxt: Crystal structure of a GDP-6-OMe-4-keto-L-xylo-heptose reductase ... -

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Basic information

Entry
Database: PDB / ID: 7cxt
TitleCrystal structure of a GDP-6-OMe-4-keto-L-xylo-heptose reductase from C.jejuni
ComponentsGDP-L-fucose synthase
KeywordsOXIDOREDUCTASE / Campylobacter jejuni C4 reductase GDP-6-OMe-4-keto-L-Xylo-heptose
Function / homology
Function and homology information


GDP-L-fucose synthase / GDP-L-fucose synthase activity / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / isomerase activity
Similarity search - Function
GDP-L-fucose synthase/GDP-L-colitose synthase / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / GDP-L-fucose synthase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKim, J.H. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Proteins / Year: 2021
Title: Crystal structure of a GDP-6-OMe-4-keto-L-xylo-heptose reductase from Campylobacter jejuni.
Authors: Kim, J.H. / Hofmann, A. / Kim, J.S.
History
DepositionSep 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: GDP-L-fucose synthase
B: GDP-L-fucose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6844
Polymers79,1932
Non-polymers1,4912
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-26 kcal/mol
Surface area27700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.328, 120.148, 58.591
Angle α, β, γ (deg.)90.000, 105.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GDP-L-fucose synthase / / GDP-4-keto-6-deoxy-D-mannose-3 / 5-epimerase-4-reductase


Mass: 39596.410 Da / Num. of mol.: 2
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: fcl, Cj1428c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0P8I6, GDP-L-fucose synthase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate trihydrate pH 5.6, 20% (w/v) polyethylene glycol 4000, 0.1 mM beta-mercaptoethanol, 1mM nicotinamide adenine dinucleotide phosphate (NADP).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.979415 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979415 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 49505 / % possible obs: 98.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.057 / Rrim(I) all: 0.15 / Χ2: 0.647 / Net I/σ(I): 3.2 / Num. measured all: 319607
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.80.45223860.820.2170.5030.45997.2
2.03-2.075.20.42524370.8470.20.4720.43497.6
2.07-2.116.10.40324970.8880.1720.4390.46699.5
2.11-2.156.30.38924840.9060.1630.4220.46199.5
2.15-2.26.50.34624500.9320.1440.3750.47599.5
2.2-2.256.60.33625010.9330.1390.3650.48699.2
2.25-2.316.60.32224820.9260.1340.3490.50399.2
2.31-2.376.50.28924310.9470.120.3130.51799.4
2.37-2.446.30.26825270.9530.1130.2910.50798.7
2.44-2.526.10.2524460.9510.1090.2730.51998.4
2.52-2.616.90.22824610.970.0930.2460.57199.4
2.61-2.716.80.20724880.970.0840.2240.57299.4
2.71-2.846.80.18924990.9760.0770.2050.59199.2
2.84-2.996.90.1624630.9820.0650.1730.64799.1
2.99-3.176.50.13924920.9850.0580.1510.71899.1
3.17-3.426.70.11724640.9890.0480.1270.83698
3.42-3.767.10.10224950.9930.0410.110.95899.6
3.76-4.316.90.09225120.9940.0370.0991.01599.1
4.31-5.436.60.08324460.9930.0350.0910.96797.6
5.43-506.80.08325440.9940.0340.090.99498.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1e7s

1e7s


Resolution: 2.05→49.549 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 1859 3.99 %
Rwork0.1654 44789 -
obs0.1673 46648 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.92 Å2 / Biso mean: 31.0493 Å2 / Biso min: 14.1 Å2
Refinement stepCycle: final / Resolution: 2.05→49.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 96 544 6210
Biso mean--36.81 35.23 -
Num. residues----696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085785
X-RAY DIFFRACTIONf_angle_d0.9757802
X-RAY DIFFRACTIONf_chiral_restr0.057846
X-RAY DIFFRACTIONf_plane_restr0.006988
X-RAY DIFFRACTIONf_dihedral_angle_d16.6793414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.05-2.10540.26531430.1944342299
2.1054-2.16740.25791420.1853481100
2.1674-2.23730.22571410.1709339899
2.2373-2.31730.21991430.1732345099
2.3173-2.41010.22021440.1677345099
2.4101-2.51980.21361430.1724339798
2.5198-2.65260.23381430.17413467100
2.6526-2.81880.23581370.1802345899
2.8188-3.03640.22081520.1768345399
3.0364-3.34190.20291400.1743341598
3.3419-3.82530.18971440.14483466100
3.8253-4.81890.17521390.1432343298
4.8189-49.5490.22751480.1662350099
Refinement TLS params.Method: refined / Origin x: -3.2129 Å / Origin y: 58.9476 Å / Origin z: 45.0395 Å
111213212223313233
T0.1739 Å20.009 Å20.0073 Å2-0.2007 Å20.006 Å2--0.194 Å2
L0.3288 °20.0199 °20.147 °2-0.1437 °20.0529 °2--0.4818 °2
S-0.01 Å °-0.0012 Å °0.0201 Å °0.0193 Å °-0.0055 Å °0.0012 Å °-0.0028 Å °0.0284 Å °0.0231 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-1 - 350
2X-RAY DIFFRACTION1allB-1 - 350
3X-RAY DIFFRACTION1allS1 - 544

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