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- PDB-6lln: citronellol catabolism dehydrogenase (AtuB) [Pseudomonas aerugino... -

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Basic information

Entry
Database: PDB / ID: 6lln
Titlecitronellol catabolism dehydrogenase (AtuB) [Pseudomonas aeruginosa PAO1]
ComponentsPutative dehydrogenase involved in catabolism of citronellol
KeywordsOXIDOREDUCTASE / Acyclic terpene utilization pathway / AtuB / Short-chain dehydrogenase/reductase(SDR) family.
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / oxidoreductase activity / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Putative dehydrogenase involved in catabolism of citronellol
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, Q. / Bartlam, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800627 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural characterization of the Pseudomonas aeruginosa dehydrogenase AtuB involved in citronellol and geraniol catabolism.
Authors: Chen, Y. / Jia, H. / Liang, Y. / Zhang, H. / Che, S. / Liu, R. / Zhang, Q. / Bartlam, M.
History
DepositionDec 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative dehydrogenase involved in catabolism of citronellol


Theoretical massNumber of molelcules
Total (without water)30,7871
Polymers30,7871
Non-polymers00
Water2,324129
1
A: Putative dehydrogenase involved in catabolism of citronellol

A: Putative dehydrogenase involved in catabolism of citronellol

A: Putative dehydrogenase involved in catabolism of citronellol

A: Putative dehydrogenase involved in catabolism of citronellol


Theoretical massNumber of molelcules
Total (without water)123,1474
Polymers123,1474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area13630 Å2
ΔGint-91 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.838, 98.152, 142.907
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-353-

HOH

21A-422-

HOH

31A-423-

HOH

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Components

#1: Protein Putative dehydrogenase involved in catabolism of citronellol


Mass: 30786.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: atuB, PA2887 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HZW0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.05 M calcium chloride dihydrate, 0.1 M MES monohydrate pH 6.0, 45% PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 23804 / % possible obs: 99.8 % / Redundancy: 12.9 % / Biso Wilson estimate: 16.44 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.021 / Net I/σ(I): 31.58
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.221 / Num. unique obs: 1155 / CC1/2: 0.99 / Rpim(I) all: 0.066 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIXv.1.17.1refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXv.1.17.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YXM

1yxm


Resolution: 1.8→49.08 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.236 1965 -
Rwork0.196 --
obs-21932 91.9 %
Refinement stepCycle: LAST / Resolution: 1.8→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 0 129 1878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631778
X-RAY DIFFRACTIONf_angle_d0.78332401
X-RAY DIFFRACTIONf_chiral_restr0.0533272
X-RAY DIFFRACTIONf_plane_restr0.0044312
X-RAY DIFFRACTIONf_dihedral_angle_d16.9991622
LS refinement shellResolution: 1.802→1.866 Å
RfactorNum. reflection% reflection
Rfree0.2609 --
Rwork0.2092 --
obs-1687 71.1 %

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