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- PDB-7bc0: Crystal structure of aldo-keto reductase from Agrobacterium tumef... -

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Basic information

Entry
Database: PDB / ID: 7bc0
TitleCrystal structure of aldo-keto reductase from Agrobacterium tumefaciens in a binary complex with NADPH
ComponentsAryl-alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / NADPH / aldo-keto reductase / sulfoquinovose
Function / homology
Function and homology information


6-dehydroglucose reductase / carbohydrate metabolic process / oxidoreductase activity
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
PHOSPHATE ION / 6-dehydroglucose reductase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2103
Polymers33,0201
Non-polymers1902
Water3,243180
1
A: Aryl-alcohol dehydrogenase
hetero molecules

A: Aryl-alcohol dehydrogenase
hetero molecules

A: Aryl-alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6299
Polymers99,0593
Non-polymers5706
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9380 Å2
ΔGint-77 kcal/mol
Surface area32480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.928, 108.928, 108.928
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-659-

HOH

21A-678-

HOH

31A-679-

HOH

41A-680-

HOH

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Components

#1: Protein Aryl-alcohol dehydrogenase /


Mass: 33019.684 Da / Num. of mol.: 1
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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2517 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M SPG 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.83→44.51 Å / Num. obs: 38236 / % possible obs: 100 % / Redundancy: 24.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.039 / Rrim(I) all: 0.193 / Net I/σ(I): 14.1
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
1.83-1.8724.94.1965874823550.4390.8544.2821100
8.97-44.4722.60.036840937210.0080.03769.299.3

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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: 1.83→44.51 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.75 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 1822 4.8 %RANDOM
Rwork0.1909 ---
obs0.1917 36384 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.59 Å2 / Biso mean: 31.964 Å2 / Biso min: 20.88 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.83→44.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 10 180 2424
Biso mean--54.1 37.31 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132281
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172171
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.633097
X-RAY DIFFRACTIONr_angle_other_deg1.4921.5754974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8675297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41921.509106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81615371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.681516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02500
LS refinement shellResolution: 1.83→1.878 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 129 -
Rwork0.305 2691 -
all-2820 -
obs--99.96 %

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