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- PDB-4jbh: 2.2A resolution structure of cobalt and zinc bound thermostable a... -

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Basic information

Entry
Database: PDB / ID: 4jbh
Title2.2A resolution structure of cobalt and zinc bound 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
: / Alcohol dehydrogenase (Zinc)
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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)155,35715
Polymers154,7534
Non-polymers60411
Water5,567309
1


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

A: Alcohol dehydrogenase (Zinc)
D: Alcohol dehydrogenase (Zinc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,35715
Polymers154,7534
Non-polymers60411
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area10190 Å2
ΔGint-89 kcal/mol
Surface area44730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.402, 125.336, 82.943
Angle α, β, γ (deg.)90.000, 107.120, 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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 25%(w/v) PEG 1500, PCB Buffer , pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.60497 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.60497 Å / Relative weight: 1
ReflectionResolution: 2.2→79.266 Å / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.1
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3469 / % possible all: 73.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å66.99 Å
Translation2.5 Å66.99 Å

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Processing

Software
NameVersionClassificationNB
SCALA0.1.27data scaling
PHASERphasing
PHENIXdev_1259refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JBG

4jbg


Resolution: 2.2→49.16 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 20.08 / Stereochemistry target values: ML
Details: Note: Friedel pairs were kept separate during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 6428 5.07 %RANDOM
Rwork0.151 ---
obs0.1533 126894 94.94 %-
all-126894 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.4 Å2 / Biso mean: 37.9155 Å2 / Biso min: 17.93 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9610 0 11 309 9930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119807
X-RAY DIFFRACTIONf_angle_d1.03213370
X-RAY DIFFRACTIONf_chiral_restr0.0781565
X-RAY DIFFRACTIONf_plane_restr0.0071741
X-RAY DIFFRACTIONf_dihedral_angle_d12.8563481
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 (%)
2.2-2.2250.28211600.24842827298768
2.225-2.25120.27521560.23933192334875
2.2512-2.27870.30862050.21763731393687
2.2787-2.30750.28251660.20563931409793
2.3075-2.33790.2281830.18564031421494
2.3379-2.36990.25732040.17774007421195
2.3699-2.40380.22132060.17494020422695
2.4038-2.43960.23892030.17424146434996
2.4396-2.47780.24012710.16413930420196
2.4778-2.51840.23952080.17224116432496
2.5184-2.56180.22672090.15994031424096
2.5618-2.60840.2232320.16254104433697
2.6084-2.65850.22972020.1684108431097
2.6585-2.71280.21292320.15474053428597
2.7128-2.77180.25042190.15764133435297
2.7718-2.83630.22962440.16234077432197
2.8363-2.90720.21022160.15384107432397
2.9072-2.98580.21412420.15654089433197
2.9858-3.07360.20822260.15614128435498
3.0736-3.17280.23152110.16144124433598
3.1728-3.28620.22892110.15344147435897
3.2862-3.41770.19142340.15294116435098
3.4177-3.57320.18552350.13534142437798
3.5732-3.76160.19522060.14824184439098
3.7616-3.99710.19671870.13894141432898
3.9971-4.30560.14861910.12374233442498
4.3056-4.73860.14812290.11424115434499
4.7386-5.42350.15562440.1334157440199
5.4235-6.83010.16562390.16534204444399
6.8301-49.17220.13232570.13044142439999

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