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- PDB-9jdq: Crystal structure of reductase EA -

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Basic information

Entry
Database: PDB / ID: 9jdq
TitleCrystal structure of reductase EA
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / short chain alcohol dehydrogenase
Function / homologyshort chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / nucleotide binding / Oxidoreductase
Function and homology information
Biological speciesExiguobacterium acetylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsTang, J. / Liuqing, C.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: crystal structure of reductase LSADH
Authors: Tang, J. / Liuqing, C.
History
DepositionSep 1, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase


Theoretical massNumber of molelcules
Total (without water)56,5462
Polymers56,5462
Non-polymers00
Water8,467470
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.747, 67.67, 74.549
Angle α, β, γ (deg.)90, 117.88, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Oxidoreductase


Mass: 28272.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence reference for source organism Exiguobacterium acetylicum.
Source: (gene. exp.) Exiguobacterium acetylicum (bacteria) / Gene: ker
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6BDS0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: peg 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.71→20 Å / Num. obs: 67589 / % possible obs: 97.65 % / Redundancy: 2 % / CC1/2: 0.75 / Net I/σ(I): 2.3
Reflection shellResolution: 1.7132→1.8362 Å / Num. unique obs: 23390 / CC1/2: 0.7 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H5X

5h5x


Resolution: 1.71→19.92 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25 3286 4.9 %RANDOM
Rwork0.23 ---
obs0.23 67589 99 %-
Refinement stepCycle: LAST / Resolution: 1.71→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 0 102 470 4416
LS refinement shellResolution: 1.713→1.757 Å
RfactorNum. reflection% reflection
Rfree0.477 --
Rwork-4188 -
obs--88.84 %

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