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

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Basic information

Entry
Database: PDB / ID: 2ewm
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 / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / (S)-1-Phenylethanol dehydrogenase
Similarity search - Component
Biological speciesAzoarcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 4, 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: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8946
Polymers53,3752
Non-polymers1,5194
Water3,009167
1
A: (S)-1-Phenylethanol dehydrogenase
B: (S)-1-Phenylethanol dehydrogenase
hetero molecules

A: (S)-1-Phenylethanol dehydrogenase
B: (S)-1-Phenylethanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,78912
Polymers106,7514
Non-polymers3,0388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_734y+2,x-2,-z-11
Buried area19860 Å2
ΔGint-175 kcal/mol
Surface area29730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.400, 58.400, 236.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-702-

SO4

21B-701-

SO4

31B-750-

HOH

Detailsthe biological assembly is the tetramer generated by a two fold axis

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Components

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


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.89 Å3/Da / Density % sol: 34.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12-18% PEG 8000, 0.05M potassium phasphate, 3% 2-methyl-2,4-pentanediol crystal was soaked with 5mM NAD+ and 5mM (R)-1-phenylethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00885 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00885 Å / Relative weight: 1
ReflectionResolution: 2.4→28 Å / Num. obs: 16156 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.073 / Rsym value: 0.08 / Net I/σ(I): 14.5
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.122 / Num. unique all: 3088 / % possible all: 86.8

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
CNXrefinement
XDSdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EW8

2ew8


Resolution: 2.4→28 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 804 -random
Rwork0.176 ---
all0.176 ---
obs0.176 15349 5 %-
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.4→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 98 167 3885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d3.61
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.292 122 -
Rwork0.205 --
obs-249 4.8 %

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