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- PDB-7u9n: S48A Horse Liver Alcohol Dehydrogenase in Complex with NADH and N... -

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Basic information

Entry
Database: PDB / ID: 7u9n
TitleS48A Horse Liver Alcohol Dehydrogenase in Complex with NADH and N-Cyclohexylformamide
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / Ternary complex
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYCLOHEXYLFORMAMIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZheng, C. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 United States
CitationJournal: Nat.Chem. / Year: 2023
Title: Enhanced active-site electric field accelerates enzyme catalysis.
Authors: Zheng, C. / Ji, Z. / Mathews, I.I. / Boxer, S.G.
History
DepositionMar 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 13, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
C: Alcohol dehydrogenase E chain
D: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,78420
Polymers160,0904
Non-polymers3,69416
Water4,792266
1
A: Alcohol dehydrogenase E chain
C: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,89210
Polymers80,0452
Non-polymers1,8478
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alcohol dehydrogenase E chain
D: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,89210
Polymers80,0452
Non-polymers1,8478
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.910, 68.656, 94.402
Angle α, β, γ (deg.)89.650, 76.000, 88.990
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Alcohol dehydrogenase E chain


Mass: 40022.453 Da / Num. of mol.: 4 / Mutation: S48A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Production host: Escherichia coli (E. coli) / References: UniProt: P00327, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-CXF / CYCLOHEXYLFORMAMIDE


Mass: 127.184 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG400(10%-25%), 2mM NADH, and 10mM N-cyclohexylformamide in Tris buffer at pH 8.20

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→38.13 Å / Num. obs: 61757 / % possible obs: 90.6 % / Redundancy: 7.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.05 / Rrim(I) all: 0.14 / Net I/σ(I): 9.7 / Num. measured all: 474125 / Scaling rejects: 58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.257.41.6283174942870.6250.6341.7491.485.1
9.83-38.137.70.06952906880.9990.0270.0742991

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWV

4dwv


Resolution: 2.2→35.93 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 3127 5.07 %
Rwork0.2132 58552 -
obs0.2155 61679 90.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.72 Å2 / Biso mean: 51.3722 Å2 / Biso min: 23.27 Å2
Refinement stepCycle: final / Resolution: 2.2→35.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11136 0 220 266 11622
Biso mean--43.87 47.88 -
Num. residues----1496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.32321300.31962389251982
2.23-2.270.3991300.30142575270587
2.27-2.310.36611350.28612477261284
2.31-2.350.33251470.27662653280090
2.35-2.390.31181410.27322757289894
2.39-2.440.34211270.27292773290094
2.44-2.50.3141610.26452734289593
2.5-2.550.29871460.25822741288793
2.55-2.620.33621500.25732706285692
2.62-2.690.34031440.25142633277791
2.69-2.770.28381390.24132642278189
2.77-2.860.3081360.23982497263385
2.86-2.960.29941570.25082737289495
2.96-3.080.3011420.2482773291594
3.08-3.220.30741560.24292731288793
3.22-3.390.28021310.23332713284492
3.39-3.60.28861530.22082608276189
3.6-3.880.20121390.21132637277690
3.88-4.270.22841540.18632764291894
4.27-4.880.20271380.16092711284992
4.88-6.150.23091190.17952613273288
6.15-35.930.17871520.15112688284092

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