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- PDB-8h2b: Crystal structure of alcohol dehydrogenase from Zobellia galactan... -

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Basic information

Entry
Database: PDB / ID: 8h2b
TitleCrystal structure of alcohol dehydrogenase from Zobellia galactanivorans
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase
Function / homology
Function and homology information


: / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / formaldehyde catabolic process / alcohol dehydrogenase / nucleotide binding / 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 domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase class 3 / S-(Hydroxymethyl)glutathione dehydrogenase
Similarity search - Component
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBrott, S. / Bornscheuer, U.T. / Nam, K.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2023
Title: Unique alcohol dehydrogenases involved in algal sugar utilization by marine bacteria
Authors: Brott, S. / Nam, K.H. / Thomas, F. / Dutschei, T. / Reisky, L. / Behrens, M. / Grimm, H.C. / Michel, G. / Schweder, T. / Bornscheuer, U.T.
History
DepositionOct 5, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)161,88818
Polymers158,6654
Non-polymers3,22314
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16780 Å2
ΔGint-223 kcal/mol
Surface area48820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.569, 92.670, 154.118
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Alcohol dehydrogenase


Mass: 39666.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0L712
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, pH 7.5, KCl and PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 76289 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.989 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 3735 / CC1/2: 0.734

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LJH

6ljh


Resolution: 2.1→49.58 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 1996 2.62 %
Rwork0.1612 74172 -
obs0.1623 76168 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.45 Å2 / Biso mean: 33.5468 Å2 / Biso min: 7.66 Å2
Refinement stepCycle: final / Resolution: 2.1→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10974 0 186 503 11663
Biso mean--29.13 36.81 -
Num. residues----1476
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.28921370.21685127526498
2.15-2.210.24141430.198252445387100
2.21-2.280.25331380.189852525390100
2.28-2.350.22941440.18152205364100
2.35-2.430.21581430.172352865429100
2.43-2.530.20881390.16552575396100
2.53-2.650.23761390.164852925431100
2.65-2.780.23261450.172252495394100
2.78-2.960.2141400.164253055445100
2.96-3.190.21321470.171953065453100
3.19-3.510.17711420.157453345476100
3.51-4.020.20391490.147753285477100
4.02-5.060.17741450.134154035548100
5.06-49.580.17841450.15815569571499

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