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- PDB-7bc1: Crystal structure of aldo-keto reductase from Agrobacterium tumef... -

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Basic information

Entry
Database: PDB / ID: 7bc1
TitleCrystal structure of aldo-keto reductase from Agrobacterium tumefaciens in a ternary complex with NADPH and glucose
ComponentsAryl-alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Aldo-keto reductase / NADPH / glucose / 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
alpha-D-glucopyranose / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 6-dehydroglucose reductase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)35,2503
Polymers34,3261
Non-polymers9242
Water4,125229
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)105,7499
Polymers102,9783
Non-polymers2,7716
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area10660 Å2
ΔGint-39 kcal/mol
Surface area31130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.853, 82.853, 77.255
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Aryl-alcohol dehydrogenase


Mass: 34326.129 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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2328458 Å3/Da / Density % sol: 44.947571 % / Description: Hexagonal plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M SPG 25% PEG 1500 In-drop protein concentration of 13 mg/ml

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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: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→52.57 Å / Num. obs: 48238 / % possible obs: 100 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.025 / Rrim(I) all: 0.086 / Net I/σ(I): 14.7 / Num. measured all: 571667 / Scaling rejects: 68
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
1.5-1.5391.672161023960.7460.5821.771.499.9
8.22-52.5711.20.03235513160.9990.010.03365.699.6

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Processing

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

7bby


Resolution: 1.5→52.51 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.001 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 2368 4.9 %RANDOM
Rwork0.1658 ---
obs0.1672 45844 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: 57.16 Å2 / Biso mean: 21.006 Å2 / Biso min: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0.59 Å2-0 Å2
2---1.19 Å20 Å2
3---3.86 Å2
Refinement stepCycle: final / Resolution: 1.5→52.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 60 229 2467
Biso mean--24.12 31.59 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132278
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172149
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.6433109
X-RAY DIFFRACTIONr_angle_other_deg1.5321.5834934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.73122.52695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70715354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2491512
X-RAY DIFFRACTIONr_chiral_restr0.0790.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02477
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 178 -
Rwork0.332 3384 -
all-3562 -
obs--99.89 %

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