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- PDB-4jbg: 1.75A resolution structure of a thermostable alcohol dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 4jbg
Title1.75A resolution structure of a thermostable alcohol dehydrogenase from Pyrobaculum aerophilum
ComponentsAlcohol dehydrogenase (Zinc)
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase / thermostability / Zinc binding
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
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 ...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
PHOSPHATE ION / Alcohol dehydrogenase (Zinc)
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsLovell, S. / Battaile, K.P. / Vitale, A. / Throne, N. / Hu, X. / Shen, M. / D'Auria, S. / Auld, D.S.
CitationJournal: Plos One / Year: 2013
Title: Physicochemical Characterization of a Thermostable Alcohol Dehydrogenase from Pyrobaculum aerophilum.
Authors: Vitale, A. / Thorne, N. / Lovell, S. / Battaile, K.P. / Hu, X. / Shen, M. / D'Auria, S. / Auld, D.S.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase (Zinc)
B: Alcohol dehydrogenase (Zinc)
C: Alcohol dehydrogenase (Zinc)
D: Alcohol dehydrogenase (Zinc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,40614
Polymers154,7534
Non-polymers65310
Water10,160564
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Alcohol dehydrogenase (Zinc)
D: Alcohol dehydrogenase (Zinc)
hetero molecules

B: Alcohol dehydrogenase (Zinc)
C: Alcohol dehydrogenase (Zinc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,40614
Polymers154,7534
Non-polymers65310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area11210 Å2
ΔGint-105 kcal/mol
Surface area44320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.509, 126.450, 84.055
Angle α, β, γ (deg.)90.000, 108.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alcohol dehydrogenase (Zinc)


Mass: 38688.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea)
Strain: ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827
Gene: PAE2687 / Plasmid: pET28-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q8ZUP0, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 20% (w/v) PEG-1000, 100 mM Tris, pH 8.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 6.1 % / Av σ(I) over netI: 8.1 / Number: 669534 / Rsym value: 0.063 / D res high: 1.822 Å / D res low: 126.253 Å / Num. obs: 109201 / % possible obs: 90.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.76126.2599.810.040.046.7
4.075.7699.810.0420.0426.6
3.334.0799.910.0460.0466.7
2.883.3399.910.0550.0556.8
2.582.8810010.0740.0746.7
2.352.5810010.0980.0986.9
2.182.3599.910.1350.1356.7
2.042.1898.910.1940.1946.3
1.922.0479.910.30.34.5
1.821.9255.910.5020.5023.7
ReflectionResolution: 1.75→79.715 Å / Num. all: 136008 / Num. obs: 136008 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6691 / % possible all: 99.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALA0.1.27data scaling
SHELXphasing
PHENIXdev_1241refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→43.99 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.75 / Phase error: 17.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1742 6837 5.03 %RANDOM
Rwork0.1515 ---
obs0.1526 135964 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.5 Å2 / Biso mean: 27.7704 Å2 / Biso min: 8.78 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9675 0 22 564 10261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099995
X-RAY DIFFRACTIONf_angle_d1.00913654
X-RAY DIFFRACTIONf_chiral_restr0.0791595
X-RAY DIFFRACTIONf_plane_restr0.0071776
X-RAY DIFFRACTIONf_dihedral_angle_d11.9633590
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.76990.25442080.221442774485100
1.7699-1.79070.26772300.214943164546100
1.7907-1.81260.24162190.213642744493100
1.8126-1.83550.22952400.201742874527100
1.8355-1.85960.22472290.196643134542100
1.8596-1.88510.2382010.194443324533100
1.8851-1.91210.24262410.182343274568100
1.9121-1.94060.20822370.179842684505100
1.9406-1.97090.20862280.17343104538100
1.9709-2.00320.21272300.163243324562100
2.0032-2.03780.19172370.162742454482100
2.0378-2.07480.20522370.163442904527100
2.0748-2.11470.1962240.156143394563100
2.1147-2.15790.18992160.15843224538100
2.1579-2.20480.19312290.157543074536100
2.2048-2.25610.17882150.147742974512100
2.2561-2.31250.16592290.138443074536100
2.3125-2.3750.16442370.137543054542100
2.375-2.44490.18572460.144143364582100
2.4449-2.52380.18022360.141942694505100
2.5238-2.6140.17392410.148343054546100
2.614-2.71870.18272360.146743044540100
2.7187-2.84240.1772460.15142774523100
2.8424-2.99220.18382310.156343474578100
2.9922-3.17960.17372200.165742714491100
3.1796-3.4250.17372470.16274308455599
3.425-3.76960.15582120.15134303451599
3.7696-4.31460.13652120.12744313452599
4.3146-5.43440.12292020.11554298450098
5.4344-44.00440.14612210.14064348456998

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