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- PDB-1f8f: CRYSTAL STRUCTURE OF BENZYL ALCOHOL DEHYDROGENASE FROM ACINETOBAC... -

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Basic information

Entry
Database: PDB / ID: 1f8f
TitleCRYSTAL STRUCTURE OF BENZYL ALCOHOL DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS
ComponentsBENZYL ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase / Rossmann fold
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / 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
ETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Benzyl alcohol dehydrogenase
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsBeauchamp, J.C. / Gillooly, D. / Warwicker, J. / Fewson, C.A. / Lapthorn, A.J.
CitationJournal: To be Published
Title: Crystal Structure of Benzyl Alcohol Dehydrogenase from Acinetobacter calcoaceticus
Authors: Beauchamp, J.C. / Gillooly, D. / Warwicker, J. / Fewson, C.A. / Lapthorn, A.J.
History
DepositionJun 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: BENZYL ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0337
Polymers39,0011
Non-polymers1,0326
Water5,567309
1
A: BENZYL ALCOHOL DEHYDROGENASE
hetero molecules

A: BENZYL ALCOHOL DEHYDROGENASE
hetero molecules

A: BENZYL ALCOHOL DEHYDROGENASE
hetero molecules

A: BENZYL ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,13228
Polymers156,0024
Non-polymers4,13024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area18790 Å2
ΔGint-371 kcal/mol
Surface area47370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.294, 96.985, 103.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BENZYL ALCOHOL DEHYDROGENASE


Mass: 39000.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59096, EC: 1.1.1.90

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Non-polymers , 5 types, 315 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#6: Water ChemComp-HOH / water / 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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG-MME2000, lithium sulphate, 2,3,4,5,6-pentafluorobenzyl alcohol, sodium acetate, zinc chloride, EDTA, NADH, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.49
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.49 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 21452 / Num. obs: 20575 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.05
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.265 / Num. unique all: 2047 / % possible all: 94.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementResolution: 2.2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Weighted ML refinement with overall anisotropic scaling and bulk solvent correction
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1044 -random 5%
Rwork0.197 ---
all0.198 21452 --
obs0.198 20575 91 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 59 309 3039
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d2.6
X-RAY DIFFRACTIONp_bond_d0.02

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