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- PDB-6iqd: Crystal structure of Alcohol dehydrogenase from Geobacillus stear... -

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Basic information

Entry
Database: PDB / ID: 6iqd
TitleCrystal structure of Alcohol dehydrogenase from Geobacillus stearothermophilus
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alcohol dehydrogenase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsXue, S. / Feng, Y. / Guo, X. / Zhao, Z.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Characterization of the substrate scope of an alcohol dehydrogenase commonly used as methanol dehydrogenase.
Authors: Guo, X. / Feng, Y. / Wang, X. / Liu, Y. / Liu, W. / Li, Q. / Wang, J. / Xue, S. / Zhao, Z.K.
History
DepositionNov 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase
B: Alcohol dehydrogenase
C: Alcohol dehydrogenase
D: Alcohol dehydrogenase
E: Alcohol dehydrogenase
F: Alcohol dehydrogenase
G: Alcohol dehydrogenase
H: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,07024
Polymers290,0238
Non-polymers1,04716
Water00
1
A: Alcohol dehydrogenase
B: Alcohol dehydrogenase
D: Alcohol dehydrogenase
F: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,53512
Polymers145,0124
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alcohol dehydrogenase
E: Alcohol dehydrogenase
G: Alcohol dehydrogenase
H: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,53512
Polymers145,0124
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Alcohol dehydrogenase
F: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7676
Polymers72,5062
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-23 kcal/mol
Surface area27280 Å2
MethodPISA
4
B: Alcohol dehydrogenase
D: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7676
Polymers72,5062
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-22 kcal/mol
Surface area27450 Å2
MethodPISA
5
C: Alcohol dehydrogenase
G: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7676
Polymers72,5062
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-23 kcal/mol
Surface area27360 Å2
MethodPISA
6
E: Alcohol dehydrogenase
H: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7676
Polymers72,5062
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-22 kcal/mol
Surface area27550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.442, 149.186, 269.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Alcohol dehydrogenase / ADH


Mass: 36252.914 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: adh / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42327, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn

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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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium sulfate, 0.1M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3350
PH range: 6.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9798 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.84→49.8 Å / Num. obs: 67992 / % possible obs: 97.68 % / Redundancy: 4.1 % / Biso Wilson estimate: 53.56 Å2 / Rmerge(I) obs: 0.1241 / Net I/σ(I): 11.53
Reflection shellResolution: 2.84→2.94 Å / Redundancy: 4 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.82 / Num. unique obs: 6314 / % possible all: 93.18

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rjw

1rjw


Resolution: 2.84→49.8 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.85
RfactorNum. reflection% reflection
Rfree0.2912 3423 5.08 %
Rwork0.2324 --
obs0.2354 67375 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.84→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20136 0 16 0 20152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320496
X-RAY DIFFRACTIONf_angle_d0.67327768
X-RAY DIFFRACTIONf_dihedral_angle_d3.22112400
X-RAY DIFFRACTIONf_chiral_restr0.053200
X-RAY DIFFRACTIONf_plane_restr0.0043584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8401-2.88070.37891440.30412457X-RAY DIFFRACTION92
2.8807-2.92370.37571400.30442494X-RAY DIFFRACTION93
2.9237-2.96930.341300.29992594X-RAY DIFFRACTION96
2.9693-3.0180.39291440.30152587X-RAY DIFFRACTION97
3.018-3.070.30681190.29922611X-RAY DIFFRACTION96
3.07-3.12590.39781500.30692609X-RAY DIFFRACTION97
3.1259-3.1860.37961430.30772593X-RAY DIFFRACTION97
3.186-3.2510.35151330.28882637X-RAY DIFFRACTION97
3.251-3.32170.37751360.28712592X-RAY DIFFRACTION97
3.3217-3.39890.32421450.28462642X-RAY DIFFRACTION97
3.3989-3.48390.35391430.28682598X-RAY DIFFRACTION98
3.4839-3.57810.35071550.26872693X-RAY DIFFRACTION98
3.5781-3.68330.35191360.26222656X-RAY DIFFRACTION99
3.6833-3.80220.32441510.25182676X-RAY DIFFRACTION99
3.8022-3.9380.33161540.24842701X-RAY DIFFRACTION99
3.938-4.09560.28251270.2222698X-RAY DIFFRACTION99
4.0956-4.28190.2551500.2062713X-RAY DIFFRACTION99
4.2819-4.50750.23891480.1892724X-RAY DIFFRACTION99
4.5075-4.78970.22471400.17462718X-RAY DIFFRACTION99
4.7897-5.15920.23511510.19342738X-RAY DIFFRACTION100
5.1592-5.67770.25631440.2172748X-RAY DIFFRACTION100
5.6777-6.49780.25341480.20762798X-RAY DIFFRACTION100
6.4978-8.18070.22231460.18612799X-RAY DIFFRACTION100
8.1807-49.98390.23621460.18082876X-RAY DIFFRACTION97

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