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- PDB-7c0e: Crystal structure of Azospirillum brasilense L-2-keto-3-deoxyarab... -

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Basic information

Entry
Database: PDB / ID: 7c0e
TitleCrystal structure of Azospirillum brasilense L-2-keto-3-deoxyarabonate dehydratase (2-oxobutyrate-bound form)
ComponentsL-2-keto-3-deoxyarabonate dehydratase
KeywordsLYASE / L-2-keto-3-deoxyarabonate dehydratase
Function / homology
Function and homology information


2-dehydro-3-deoxy-L-arabinonate dehydratase / 2-dehydro-3-deoxy-L-arabinonate dehydratase activity / L-arabinose catabolic process to 2-oxoglutarate / 4-hydroxy-tetrahydrodipicolinate synthase activity / protein homodimerization activity / cytosol
Similarity search - Function
DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
L-2-keto-3-deoxyarabonate dehydratase
Similarity search - Component
Biological speciesAzospirillum brasilense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsWatanabe, Y. / Ono, A. / Watanabe, S.
CitationJournal: Biochemistry / Year: 2020
Title: Biochemical and Structural Characterization of l-2-Keto-3-deoxyarabinonate Dehydratase: A Unique Catalytic Mechanism in the Class I Aldolase Protein Superfamily.
Authors: Watanabe, S. / Watanabe, Y. / Nobuchi, R. / Ono, A.
History
DepositionMay 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 29, 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: L-2-keto-3-deoxyarabonate dehydratase
B: L-2-keto-3-deoxyarabonate dehydratase
C: L-2-keto-3-deoxyarabonate dehydratase
D: L-2-keto-3-deoxyarabonate dehydratase
E: L-2-keto-3-deoxyarabonate dehydratase
F: L-2-keto-3-deoxyarabonate dehydratase
G: L-2-keto-3-deoxyarabonate dehydratase
H: L-2-keto-3-deoxyarabonate dehydratase
I: L-2-keto-3-deoxyarabonate dehydratase
J: L-2-keto-3-deoxyarabonate dehydratase
K: L-2-keto-3-deoxyarabonate dehydratase
L: L-2-keto-3-deoxyarabonate dehydratase


Theoretical massNumber of molelcules
Total (without water)421,83512
Polymers421,83512
Non-polymers00
Water20,3931132
1
A: L-2-keto-3-deoxyarabonate dehydratase
B: L-2-keto-3-deoxyarabonate dehydratase
C: L-2-keto-3-deoxyarabonate dehydratase
D: L-2-keto-3-deoxyarabonate dehydratase


Theoretical massNumber of molelcules
Total (without water)140,6124
Polymers140,6124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-44 kcal/mol
Surface area39020 Å2
MethodPISA
2
E: L-2-keto-3-deoxyarabonate dehydratase
F: L-2-keto-3-deoxyarabonate dehydratase
G: L-2-keto-3-deoxyarabonate dehydratase
H: L-2-keto-3-deoxyarabonate dehydratase


Theoretical massNumber of molelcules
Total (without water)140,6124
Polymers140,6124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11330 Å2
ΔGint-45 kcal/mol
Surface area38550 Å2
MethodPISA
3
I: L-2-keto-3-deoxyarabonate dehydratase
J: L-2-keto-3-deoxyarabonate dehydratase
K: L-2-keto-3-deoxyarabonate dehydratase
L: L-2-keto-3-deoxyarabonate dehydratase


Theoretical massNumber of molelcules
Total (without water)140,6124
Polymers140,6124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-40 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.524, 81.198, 142.835
Angle α, β, γ (deg.)85.710, 88.430, 75.390
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
L-2-keto-3-deoxyarabonate dehydratase / L-KDA dehydratase / 2-dehydro-3-deoxy-L-arabinonate dehydratase / L-2-keto-3-deoxyarabinonate dehydratase


Mass: 35152.902 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum brasilense (bacteria) / Gene: araD / Production host: Escherichia coli (E. coli)
References: UniProt: Q1JUQ0, 2-dehydro-3-deoxy-L-arabinonate dehydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1132 / 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 % sol: 37.57 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, 22-27% PEG 3350
PH range: 8.3-8.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.954 Å / Num. obs: 160387 / % possible obs: 95.9 % / Redundancy: 2.266 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.166 / Χ2: 1.146 / Net I/σ(I): 5.54 / Num. measured all: 709648
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.342.220.6931.1611103352870500180.5290.90294.6
2.34-2.52.2790.5021.6310809049424474340.6890.65296
2.5-2.72.3110.3652.310242346196443170.8060.47495.9
2.7-2.952.1980.2493.238960542464407600.8980.32596
2.95-3.32.3360.1545.348621638390369000.9580.296.1
3.3-3.812.2270.0898.877293933860327560.9840.11696.7
3.81-4.662.3170.06213.086421528670277100.9910.08196.7
4.66-6.562.2330.0613.24772522164213690.9920.07896.4
6.56-47.9542.2970.03919.522740212404119320.9970.05196.2

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C0C

7c0c


Resolution: 2.204→47.954 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 29.34 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2691 8082 5.04 %
Rwork0.221 152305 -
obs0.2235 160387 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.03 Å2 / Biso mean: 35.5377 Å2 / Biso min: 12.76 Å2
Refinement stepCycle: final / Resolution: 2.204→47.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27979 0 0 1132 29111
Biso mean---33.92 -
Num. residues----3637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328619
X-RAY DIFFRACTIONf_angle_d0.62138938
X-RAY DIFFRACTIONf_chiral_restr0.0434344
X-RAY DIFFRACTIONf_plane_restr0.0055167
X-RAY DIFFRACTIONf_dihedral_angle_d14.72417249
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.204-2.22880.35622510.2946481694
2.2288-2.2550.36192440.2866510397
2.255-2.28250.33622420.2806503298
2.2825-2.31140.33712430.2718513298
2.3114-2.34180.3312900.2669499398
2.3418-2.37390.31842550.2688502998
2.3739-2.40780.3522560.2619512998
2.4078-2.44380.27762700.2502500598
2.4438-2.4820.29812580.2475510198
2.482-2.52270.3162550.2438502298
2.5227-2.56610.30672900.2451512798
2.5661-2.61280.31122880.2445501098
2.6128-2.66310.2912640.2501506098
2.6631-2.71740.32812770.243507198
2.7174-2.77650.28472640.2409509898
2.7765-2.84110.30552730.2377503798
2.8411-2.91210.32172570.2358516299
2.9121-2.99080.28072770.2342508699
2.9908-3.07880.30053210.2312503099
3.0788-3.17820.26652800.2245506899
3.1782-3.29180.27872560.2217509299
3.2918-3.42350.26472960.2123512899
3.4235-3.57930.25712870.2071508299
3.5793-3.76790.23682650.1964509699
3.7679-4.00390.26322340.2516099
4.0039-4.31280.24462730.1944515299
4.3128-4.74650.22712750.1925511299
4.7465-5.43250.2452730.2059512999
5.4325-6.84120.23192800.21195139100
6.8412-47.9540.19812880.1854510499

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