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- PDB-2ew8: Crystal Structure of the (S)-Specific 1-Phenylethanol Dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 2ew8
TitleCrystal Structure of the (S)-Specific 1-Phenylethanol Dehydrogenase of the Denitrifying Bacterium Strain EbN1
Components(S)-1-Phenylethanol dehydrogenase
KeywordsTRANSFERASE / Dehydrogenase
Function / homology
Function and homology information


(S)-1-phenylethanol dehydrogenase / anaerobic ethylbenzene catabolic process / 1-phenylethanol dehydrogenase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / protein homotetramerization / nucleotide binding
Similarity search - Function
: / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / (S)-1-Phenylethanol dehydrogenase
Similarity search - Component
Biological speciesAzoarcus sp. EbN1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHoeffken, H.W.
CitationJournal: Biochemistry / Year: 2006
Title: Crystal Structure and Enzyme kinetics of the (S)-Specific 1-Phenylethanol Dehydrogenase of the denitrifying bacterium Strain EbN1
Authors: Hoeffken, H.W. / Duong, M. / Friedrich, T. / Breuer, M. / Hauer, B. / Reinhardt, R. / Rabus, R. / Heider, J.
History
DepositionNov 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 23, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: (S)-1-Phenylethanol dehydrogenase
B: (S)-1-Phenylethanol dehydrogenase
C: (S)-1-Phenylethanol dehydrogenase
D: (S)-1-Phenylethanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9436
Polymers106,7514
Non-polymers1922
Water11,007611
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14600 Å2
ΔGint-98 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.6, 110.7, 77.3
Angle α, β, γ (deg.)90, 116.31, 90
Int Tables number5
Space group name H-MC121
Detailsthe biological assembly is the tetramer in the assymetric unit

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Components

#1: Protein
(S)-1-Phenylethanol dehydrogenase


Mass: 26687.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azoarcus sp. EbN1 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: GenBank: 56476740, UniProt: Q5P5I4*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% PEG 8000, 0.05 M potassium phosphate, 3% 2-methyl-2,4-pentandiol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Details: GOEBEL MIRROR
RadiationMonochromator: goebel mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→58.5 Å / Num. all: 57063 / Num. obs: 56645 / % possible obs: 98.22 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.063 / Rsym value: 0.076 / Net I/σ(I): 5.92
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.75 / Num. unique all: 5409 / Rsym value: 0.216 / % possible all: 98.22

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Processing

Software
NameClassification
smartdata collection
SAINTdata reduction
CNXrefinement
SMARTdata reduction
SAINTdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I01

1i01


Resolution: 2.1→58.6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 4250 -random
Rwork0.171 ---
all0.171 57063 --
obs0.171 56112 7.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→58.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6890 0 10 611 7511
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009
RfactorNum. reflection% reflection
Rfree0.249 704 -
Rwork0.214 --
obs-8309 7.8 %

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