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- PDB-9jdt: Crystal structure of reductase NaAD -

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Basic information

Entry
Database: PDB / ID: 9jdt
TitleCrystal structure of reductase NaAD
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / short chain alcohol dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
: / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans DSM 12444 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 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
Revision 1.1Mar 11, 2026Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
E: Short-chain dehydrogenase/reductase SDR
F: Short-chain dehydrogenase/reductase SDR
G: Short-chain dehydrogenase/reductase SDR
H: Short-chain dehydrogenase/reductase SDR
I: Short-chain dehydrogenase/reductase SDR
J: Short-chain dehydrogenase/reductase SDR
K: Short-chain dehydrogenase/reductase SDR
L: Short-chain dehydrogenase/reductase SDR
M: Short-chain dehydrogenase/reductase SDR
N: Short-chain dehydrogenase/reductase SDR
O: Short-chain dehydrogenase/reductase SDR
P: Short-chain dehydrogenase/reductase SDR


Theoretical massNumber of molelcules
Total (without water)444,86216
Polymers444,86216
Non-polymers00
Water2,918162
1
A: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
E: Short-chain dehydrogenase/reductase SDR
G: Short-chain dehydrogenase/reductase SDR


Theoretical massNumber of molelcules
Total (without water)111,2164
Polymers111,2164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-104 kcal/mol
Surface area33090 Å2
MethodPISA
2
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
F: Short-chain dehydrogenase/reductase SDR
H: Short-chain dehydrogenase/reductase SDR


Theoretical massNumber of molelcules
Total (without water)111,2164
Polymers111,2164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-103 kcal/mol
Surface area33150 Å2
MethodPISA
3
I: Short-chain dehydrogenase/reductase SDR
K: Short-chain dehydrogenase/reductase SDR
M: Short-chain dehydrogenase/reductase SDR
O: Short-chain dehydrogenase/reductase SDR


Theoretical massNumber of molelcules
Total (without water)111,2164
Polymers111,2164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-101 kcal/mol
Surface area33150 Å2
MethodPISA
4
J: Short-chain dehydrogenase/reductase SDR
L: Short-chain dehydrogenase/reductase SDR
N: Short-chain dehydrogenase/reductase SDR
P: Short-chain dehydrogenase/reductase SDR


Theoretical massNumber of molelcules
Total (without water)111,2164
Polymers111,2164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-100 kcal/mol
Surface area33210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.317, 121.768, 276.149
Angle α, β, γ (deg.)90, 93.4, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Short-chain dehydrogenase/reductase SDR


Mass: 27803.887 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans DSM 12444 (bacteria)
Gene: Saro_3543
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A4XEP2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.71 %
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: 3.26→110 Å / Num. obs: 54761 / % possible obs: 97.65 % / Redundancy: 2 % / CC1/2: 0.75 / Net I/σ(I): 2.3
Reflection shellResolution: 3.2644→3.5368 Å / Num. unique obs: 11191 / CC1/2: 0.8

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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: 3.26→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.3 2804 5.1 %RANDOM
Rwork0.26 ---
obs-54761 99 %-
Refinement stepCycle: LAST / Resolution: 3.26→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29605 0 0 162 29767
LS refinement shellResolution: 3.265→3.349 Å
RfactorNum. reflection% reflection
Rfree0.42 182 -
Rwork0.297 3642 -
obs--78.06 %

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