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- PDB-4z6k: Alcohol dehydrogenase from the antarctic psychrophile Moraxella s... -

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Basic information

Entry
Database: PDB / ID: 4z6k
TitleAlcohol dehydrogenase from the antarctic psychrophile Moraxella sp. TAE 123
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Cold-adapted enzyme / NAD-dependent alcohol dehydrogenase / Zinc-binding protein
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 / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...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 / 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 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alcohol dehydrogenase
Similarity search - Component
Biological speciesMoraxella sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsPapanikolau, Y. / Bouriotis, V. / Petratos, K.
Citation
Journal: Acs Omega / Year: 2020
Title: Structure and Dynamics of a Thermostable Alcohol Dehydrogenase from the Antarctic Psychrophile Moraxella sp. TAE123
Authors: Petratos, K. / Gessmann, R. / Daskalakis, V. / Papadovasilaki, M. / Papanikolau, Y. / Tsigos, I. / Bouriotis, V.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2005
Title: Crystallization and preliminary X-ray diffraction studies of an alcohol dehydrogenase from the Antarctic psychrophile Moraxella sp. TAE123.
Authors: Papanikolau, Y. / Tsigos, I. / Papadovasilaki, M. / Bouriotis, V. / Petratos, K.
History
DepositionApr 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: 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.title / _citation.year

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,42114
Polymers146,7674
Non-polymers65410
Water17,925995
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9710 Å2
ΔGint-91 kcal/mol
Surface area51420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.573, 136.573, 210.832
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 339
2010B1 - 339
1020A1 - 345
2020C1 - 345
1030A1 - 339
2030D1 - 339
1040B1 - 339
2040C1 - 339
1050B1 - 340
2050D1 - 340
1060C1 - 339
2060D1 - 339

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Alcohol dehydrogenase /


Mass: 36691.785 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella sp. (strain TAE123) (bacteria)
Gene: adh / Plasmid: pET-26b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8GIX7, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 995 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68 % / Description: Truncated hexagonal bipyramids
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: reservoir solution: 100 mM Bis-Tris, 2 M ammonium sulphate, 100 mM NaCl, 100 mM imidazole. hanging drop volume 8 microL of protein and reservoir solutions (3:1).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: May 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→118.34 Å / Num. obs: 171943 / % possible obs: 96.63 % / Redundancy: 10 % / Rsym value: 0.093 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→1.95 Å / % possible all: 72.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→118.34 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 9.198 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23294 8613 5 %RANDOM
Rwork0.21045 ---
obs0.21158 163330 96.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.121 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20.62 Å2-0 Å2
2--1.24 Å20 Å2
3----4.03 Å2
Refinement stepCycle: 1 / Resolution: 1.9→118.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10148 0 10 995 11153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01910396
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.95414133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04851372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75825.245408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.747151683
X-RAY DIFFRACTIONr_chiral_restr0.1190.21629
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02111916
X-RAY DIFFRACTIONr_gen_planes_other0.0150.022196
X-RAY DIFFRACTIONr_mcbond_it2.6632.7255490
X-RAY DIFFRACTIONr_mcbond_other2.6362.7245489
X-RAY DIFFRACTIONr_mcangle_it3.5614.5766860
X-RAY DIFFRACTIONr_mcangle_other3.5654.5776861
X-RAY DIFFRACTIONr_scbond_it3.5563.1244905
X-RAY DIFFRACTIONr_scbond_other3.5533.1224903
X-RAY DIFFRACTIONr_scangle_other4.8955.1017273
X-RAY DIFFRACTIONr_long_range_B_refined10.9576.97812626
X-RAY DIFFRACTIONr_long_range_B_other10.9286.62212230
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A207960.05
12B207960.05
21A212750.03
22C212750.03
31A208700.04
32D208700.04
41B207460.05
42C207460.05
51B208910.05
52D208910.05
61C208080.05
62D208080.05
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 453 -
Rwork0.418 8445 -
obs--72.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.36480.90670.19491.86780.72912.05050.0143-0.15760.15320.1105-0.13160.0589-0.334-0.08960.11720.4609-0.1984-0.13710.12610.03620.3988-29.81990.78339.401
24.40580.39951.0882.6083-0.37213.8519-0.02240.40940.5729-0.0442-0.09780.2163-0.8304-0.24220.12010.4393-0.0726-0.10520.32740.05190.4281-37.20891.14911.068
31.71071.98780.82243.11182.09032.6368-0.19670.2150.3708-0.41130.07360.224-0.77620.09630.1230.5517-0.2339-0.17450.23280.10990.4438-23.23999.3830.22
41.65270.3341-1.05011.13660.3092.4246-0.03820.3037-0.07610.0869-0.0293-0.1238-0.08140.07860.06750.0347-0.1111-0.00910.5532-0.10690.4049-29.86660.56-13.598
52.14150.42420.31213.1206-1.53225.94750.05790.1405-0.44320.146-0.2428-0.5780.42070.76280.1850.1783-0.1018-0.07590.40570.01710.527-19.39861.93313.737
63.7352-1.2121-2.30713.25652.6373.1616-0.0009-0.0017-0.17680.00360.1169-0.5049-0.17840.5119-0.11610.1011-0.1433-0.04320.62170.01690.4405-17.9664.179-8.954
72.90570.57140.55091.5748-0.06251.8013-0.11630.26350.1151-0.0872-0.01530.1572-0.1965-0.32190.13160.08-0.0428-0.06430.6182-0.13560.4099-63.79671.399-7.025
83.43421.28640.19383.63551.2964.10790.0483-0.07580.47240.3954-0.18160.4297-0.5743-0.71890.13320.3103-0.0068-0.00730.4994-0.10950.4468-60.36977.67221.304
94.35290.32721.56910.731-0.41022.0118-0.182-0.41790.41650.15210.0670.2575-0.2603-0.67410.11490.1341-0.0405-0.0160.7582-0.20240.4646-74.49969.9842.371
101.82960.5076-0.54261.4268-0.94512.9160.0778-0.0831-0.18860.2403-0.1598-0.00770.1785-0.08380.08210.4938-0.2721-0.07410.15210.06290.4179-37.2456.06646.412
112.966-0.0609-0.91482.06220.95136.1691-0.03130.2572-0.69660.2108-0.1474-0.08350.8463-0.1150.17880.3229-0.2012-0.00780.2833-0.08530.5187-43.94447.89119.12
122.0383-0.26350.47754.6077-2.87043.37340.00620.0402-0.550.02740.03520.10010.5271-0.4565-0.04150.4884-0.32040.01730.2994-0.05040.4909-46.44447.52341.546
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 151
2X-RAY DIFFRACTION2A152 - 287
3X-RAY DIFFRACTION3A288 - 345
4X-RAY DIFFRACTION4B1 - 152
5X-RAY DIFFRACTION5B153 - 286
6X-RAY DIFFRACTION6B287 - 340
7X-RAY DIFFRACTION7C1 - 148
8X-RAY DIFFRACTION8C149 - 287
9X-RAY DIFFRACTION9C288 - 345
10X-RAY DIFFRACTION10D1 - 148
11X-RAY DIFFRACTION11D149 - 286
12X-RAY DIFFRACTION12D287 - 340

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