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- PDB-5uib: Crystal Structure of an Oxidoreductase from Agrobacterium radioba... -

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Basic information

Entry
Database: PDB / ID: 5uib
TitleCrystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, L-tartaric acid and Magnesium
ComponentsOxidoreductase protein
KeywordsOXIDOREDUCTASE / L-tartrate
Function / homology
Function and homology information


D-apiose dehydrogenase / oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L(+)-TARTARIC ACID / D-apiose dehydrogenase
Similarity search - Component
Biological speciesAgrobacterium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsCook, W.J. / Fedorov, A.A. / Fedorov, E.V. / Huang, H. / Bonanno, J.B. / Gerlt, J.A. / Almo, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118303 United States
CitationJournal: To be published
Title: Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, L-tartaric acid and Magnesium
Authors: Cook, W.J. / Fedorov, A.A. / Fedorov, E.V. / Huang, H. / Bonanno, J.B. / Gerlt, J.A. / Almo, S.C.
History
DepositionJan 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase protein
B: Oxidoreductase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6518
Polymers74,9752
Non-polymers1,6766
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-35 kcal/mol
Surface area24780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.622, 113.109, 65.820
Angle α, β, γ (deg.)90.00, 94.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Oxidoreductase protein


Mass: 37487.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium radiobacter (strain K84 / ATCC BAA-868) (bacteria)
Strain: K84 / ATCC BAA-868 / Gene: Arad_9238 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9JK80
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5 M Sodium formate, 5 mM NAD+, 5 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2016 / Details: Diamond
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.65→29.6 Å / Num. obs: 29362 / % possible obs: 99.4 % / Redundancy: 3.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.094 / Rrim(I) all: 0.137 / Net I/σ(I): 5.5
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4299 / CC1/2: 0.538 / Rpim(I) all: 0.772 / Rrim(I) all: 1.134 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.21data scaling
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UHW

5uhw


Resolution: 2.65→26.6 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.905 / SU B: 29.189 / SU ML: 0.263 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.497 / ESU R Free: 0.282 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23881 1468 5 %RANDOM
Rwork0.20424 ---
obs0.20594 27812 99.34 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 56.159 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å2-0 Å2-0.11 Å2
2---0.71 Å2-0 Å2
3---1.51 Å2
Refinement stepCycle: 1 / Resolution: 2.65→26.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 110 22 5317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195407
X-RAY DIFFRACTIONr_bond_other_d0.0020.024933
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9647351
X-RAY DIFFRACTIONr_angle_other_deg0.9311405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0145682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36424230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30315844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7891533
X-RAY DIFFRACTIONr_chiral_restr0.0670.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021130
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7123.5262734
X-RAY DIFFRACTIONr_mcbond_other0.7123.5252733
X-RAY DIFFRACTIONr_mcangle_it1.2575.2863414
X-RAY DIFFRACTIONr_mcangle_other1.2575.2873415
X-RAY DIFFRACTIONr_scbond_it0.6073.6562673
X-RAY DIFFRACTIONr_scbond_other0.6063.6552670
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.085.4613936
X-RAY DIFFRACTIONr_long_range_B_refined2.51742.1865926
X-RAY DIFFRACTIONr_long_range_B_other2.51742.1865926
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 123 -
Rwork0.348 2028 -
obs--99.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.80040.083-0.15311.33470.54161.41130.1341-0.07350.03530.2156-0.1574-0.02570.2032-0.02670.02330.2188-0.07420.04170.29720.00630.01318.1087-30.953415.332
20.4478-0.5883-0.23471.65770.43080.54570.19430.183-0.0291-0.0681-0.22410.00260.0369-0.08180.02980.24020.0860.00970.3587-0.01880.011424.2782-55.9111-19.7694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 345
2X-RAY DIFFRACTION2B4 - 345

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