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- PDB-7cok: Crystal structure of ligand-free form of 5-ketofructose reductase... -

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Basic information

Entry
Database: PDB / ID: 7cok
TitleCrystal structure of ligand-free form of 5-ketofructose reductase of Gluconobacter sp. strain CHM43
Components5-ketofructose reductase
KeywordsOXIDOREDUCTASE / Gluconobacter / reductase / 5-ketofructose
Biological speciesGluconobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNoda, S. / Hodoya, Y. / Nguyen, T.M. / Kataoka, N. / Adachi, O. / Matsutani, M. / Matsushita, K. / Yakushi, T. / Goto, M.
CitationJournal: J.Bacteriol. / Year: 2021
Title: The 5-Ketofructose Reductase of Gluconobacter sp. Strain CHM43 Is a Novel Class in the Shikimate Dehydrogenase Family.
Authors: Nguyen, T.M. / Goto, M. / Noda, S. / Matsutani, M. / Hodoya, Y. / Kataoka, N. / Adachi, O. / Matsushita, K. / Yakushi, T.
History
DepositionAug 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 6, 2021Group: 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 1.3Nov 29, 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: 5-ketofructose reductase
B: 5-ketofructose reductase


Theoretical massNumber of molelcules
Total (without water)59,0292
Polymers59,0292
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-16 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.527, 63.475, 93.919
Angle α, β, γ (deg.)90.000, 93.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 5-ketofructose reductase


Mass: 29514.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter sp. (bacteria) / Strain: CHM43 / Plasmid: pBBR1MCS-4 / Production host: Gluconobacter sp. (bacteria) / Strain (production host): CHM43
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3350, HEPES-Na, calcium acetate, ethylene glycol, 1,4-butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.5→93.751 Å / Num. all: 77600 / Num. obs: 77600 / % possible obs: 99.5 % / Redundancy: 4.5 % / Rpim(I) all: 0.05 / Rrim(I) all: 0.107 / Rsym value: 0.094 / Net I/av σ(I): 4.5 / Net I/σ(I): 9.4 / Num. measured all: 351914
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.584.70.511.153236113410.2660.5770.513.699.8
1.58-1.684.70.3631.849990107350.190.4110.3634.499.9
1.68-1.794.60.2632.546346100530.1390.2980.2635.599.8
1.79-1.944.50.1843.74210293620.0990.2090.1847.499.6
1.94-2.124.10.13553507485820.0770.1560.1359.699.4
2.12-2.374.20.1076.33232577850.0590.1230.10712.199.1
2.37-2.744.70.0966.83249368650.050.1080.09614.899.1
2.74-3.354.70.0857.62761358150.0440.0960.08517.399.2
3.35-4.744.70.0728.82145345400.0380.0820.07219.799.2
4.74-41.4534.50.05710.71128225220.030.0650.05718.498.8

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NVT

1nvt


Resolution: 1.5→41.45 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.917 / SU B: 1.618 / SU ML: 0.063 / SU R Cruickshank DPI: 0.0967 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 3862 5 %RANDOM
Rwork0.2319 ---
obs0.2331 73708 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 47.15 Å2 / Biso mean: 17.951 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.5→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 0 231 4223
Biso mean---24.45 -
Num. residues----555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194054
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9595513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3645553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.78825140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41415641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5041517
X-RAY DIFFRACTIONr_chiral_restr0.090.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212979
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 291 -
Rwork0.224 5482 -
all-5773 -
obs--99.62 %

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