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- PDB-7bbz: Crystal structure of apo aldo-keto reductase from Agrobacterium t... -

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Basic information

Entry
Database: PDB / ID: 7bbz
TitleCrystal structure of apo aldo-keto reductase from Agrobacterium tumefaciens
ComponentsAryl-alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / aldo-keto reductase / trimeric / apo / sulfoquinovose
Function / homology
Function and homology information


6-dehydroglucose reductase / oxidoreductase activity / cytosol
Similarity search - Function
: / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
6-dehydroglucose reductase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsSnow, A. / Sharma, M. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2017-190 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria.
Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / ...Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / Ascher, D.B. / McConville, M.J. / Davies, G.J. / Williams, S.J. / Goddard-Borger, E.D.
History
DepositionDec 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aryl-alcohol dehydrogenase
B: Aryl-alcohol dehydrogenase
C: Aryl-alcohol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)102,9783
Polymers102,9783
Non-polymers00
Water9,530529
1
A: Aryl-alcohol dehydrogenase
B: Aryl-alcohol dehydrogenase

C: Aryl-alcohol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)102,9783
Polymers102,9783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_445x-1/2,-y-1/2,-z1
Buried area6020 Å2
ΔGint-25 kcal/mol
Surface area32140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.341, 137.547, 153.843
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Aryl-alcohol dehydrogenase


Mass: 34326.129 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / Gene: Atu3278 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CEY6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.298 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium Malonate dibasic monohydrate 0.1M bis-tris propane 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.77→53.73 Å / Num. obs: 92257 / % possible obs: 100 % / Redundancy: 8.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.045 / Rrim(I) all: 0.128 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.77-1.88.31.8763757245110.5470.7092.0081.2100
9.69-53.677.70.04849606440.9990.0180.05134.699.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BBY

7bby


Resolution: 1.77→53.67 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.936 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 4576 5 %RANDOM
Rwork0.1794 ---
obs0.1809 87639 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.59 Å2 / Biso mean: 27.112 Å2 / Biso min: 11.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å20 Å2
2---2.4 Å20 Å2
3---0.42 Å2
Refinement stepCycle: final / Resolution: 1.77→53.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6673 0 0 530 7203
Biso mean---32.26 -
Num. residues----894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136804
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176571
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.6319244
X-RAY DIFFRACTIONr_angle_other_deg1.4331.57815075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85621.801311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.036151125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2821546
X-RAY DIFFRACTIONr_chiral_restr0.0780.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027754
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021482
LS refinement shellResolution: 1.77→1.816 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 331 -
Rwork0.302 6448 -
all-6779 -
obs--99.9 %

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