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- PDB-7col: Crystal structure of 5-ketofructose reductase complexed with NADPH -

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Basic information

Entry
Database: PDB / ID: 7col
TitleCrystal structure of 5-ketofructose reductase complexed with NADPH
Components5-ketofructose reductase
KeywordsOXIDOREDUCTASE / Gluconobacter / reductase / 5-ketofructose
Function / homologyChem-NDP
Function and homology information
Biological speciesGluconobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHodoya, Y. / Noda, S. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5204
Polymers59,0292
Non-polymers1,4912
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-15 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.500, 61.528, 96.855
Angle α, β, γ (deg.)90.000, 96.820, 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: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, HEPES-Na, Ammonium fluoride, MPD

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→96.169 Å / Num. all: 33451 / Num. obs: 33451 / % possible obs: 96.7 % / Redundancy: 3.2 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.072 / Rsym value: 0.06 / Net I/av σ(I): 7.4 / Net I/σ(I): 13.1 / Num. measured all: 105580
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
1.95-2.0630.1515.11391646790.1030.1840.1516.393.1
2.06-2.183.20.1136.61487246860.0740.1360.1138.499
2.18-2.333.10.0917.91376843770.0610.110.09110.597.8
2.33-2.523.20.0788.91310841170.0510.0930.07811.798.5
2.52-2.763.20.079.31197237630.0460.0840.0713.598.2
2.76-3.083.20.05910.31085834040.0390.0710.0591697.5
3.08-3.563.20.05410.9945229560.0350.0650.05418.796.6
3.56-4.363.20.05111.6803124990.0330.0610.05120.895.7
4.36-6.173.20.05110.9624219240.0320.060.05121.294.7
6.17-37.8873.20.0511336110460.0320.060.0521.391.7

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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: 1.95→40.21 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.273 / SU ML: 0.149 / SU R Cruickshank DPI: 0.2399 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2637 1723 5.2 %RANDOM
Rwork0.2085 ---
obs0.2113 31710 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.87 Å2 / Biso mean: 24.366 Å2 / Biso min: 12.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0 Å2-1.36 Å2
2---0.17 Å2-0 Å2
3---1.22 Å2
Refinement stepCycle: final / Resolution: 1.95→40.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 96 399 4500
Biso mean--33.97 33.31 -
Num. residues----558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194170
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9895690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5295556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.64324.929140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00115640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4031518
X-RAY DIFFRACTIONr_chiral_restr0.0880.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213036
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 106 -
Rwork0.251 2118 -
all-2224 -
obs--87.39 %

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