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- PDB-7c0c: Crystal structure of Azospirillum brasilense L-2-keto-3-deoxyarab... -

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Basic information

Entry
Database: PDB / ID: 7c0c
TitleCrystal structure of Azospirillum brasilense L-2-keto-3-deoxyarabonate dehydratase (apo 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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
L-2-keto-3-deoxyarabonate dehydratase
Similarity search - Component
Biological speciesAzospirillum brasilense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWatanabe, Y. / Nobuchi, R. / 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)420,83812
Polymers420,83812
Non-polymers00
Water31,7781764
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)140,2794
Polymers140,2794
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
ΔGint-38 kcal/mol
Surface area38990 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)140,2794
Polymers140,2794
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11330 Å2
ΔGint-40 kcal/mol
Surface area38800 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)140,2794
Polymers140,2794
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11160 Å2
ΔGint-40 kcal/mol
Surface area39350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.394, 81.812, 144.419
Angle α, β, γ (deg.)85.470, 87.860, 75.620
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: 35069.836 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


Mass: 18.015 Da / Num. of mol.: 1764 / 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: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 253500 / % possible obs: 97.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.086 / Rrim(I) all: 0.163 / Χ2: 2.53 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.933.80.829125240.6290.4950.9661.27796.1
1.93-1.973.80.706126000.690.4210.8231.33596.4
1.97-2.013.80.598125070.7610.3550.6961.36896.2
2.01-2.053.80.517126340.7950.3070.6021.42496.5
2.05-2.093.80.45125600.8330.2670.5231.51396.5
2.09-2.143.80.405125750.8590.240.4711.59196.7
2.14-2.193.80.347125830.8930.2060.4031.69196.9
2.19-2.253.80.325126560.9010.1930.3781.75297.1
2.25-2.323.80.286126310.9180.170.3331.92697.1
2.32-2.393.80.261127130.9310.1550.3042.0597.4
2.39-2.483.80.235127490.9420.140.2732.23497.8
2.48-2.583.80.212127850.9460.1270.2482.53297.8
2.58-2.73.80.198127180.9530.1190.2322.70198.1
2.7-2.843.80.178128120.9610.1070.2083.08198.1
2.84-3.023.70.16128040.9650.0970.1873.45598.3
3.02-3.253.60.136127900.9750.0840.163.94898.2
3.25-3.583.50.113128290.9820.0720.1354.43898.2
3.58-4.093.30.09127120.9860.0590.1084.77397.6
4.09-5.163.10.073126880.9890.050.0894.71497.5
5.16-503.30.062126300.9930.0410.0754.30297

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FKK

3fkk


Resolution: 1.9→40.44 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.75
RfactorNum. reflection% reflection
Rfree0.2974 12868 5.08 %
Rwork0.2524 --
obs0.2547 253464 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.6 Å2 / Biso mean: 31.624 Å2 / Biso min: 9.91 Å2
Refinement stepCycle: final / Resolution: 1.9→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28006 0 0 1764 29770
Biso mean---29.63 -
Num. residues----3640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328647
X-RAY DIFFRACTIONf_angle_d0.60938975
X-RAY DIFFRACTIONf_chiral_restr0.0424348
X-RAY DIFFRACTIONf_plane_restr0.0045171
X-RAY DIFFRACTIONf_dihedral_angle_d14.65617270
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.91910.39452720.3404521363
1.9191-1.94170.40034600.3339801796
1.9417-1.96530.37254170.3222804296
1.9653-1.99020.39223990.3165807196
1.9902-2.01640.34074340.3085802396
2.0164-2.0440.35764570.3055805896
2.044-2.07320.35334390.3061794097
2.0732-2.10420.37364570.3004811596
2.1042-2.1370.3614480.2889802197
2.137-2.17210.32954700.2867800897
2.1721-2.20950.31414150.2783818997
2.2095-2.24970.33944330.2796806397
2.2497-2.2930.31244040.2787814797
2.293-2.33980.32084130.2687811297
2.3398-2.39060.33494170.2832815898
2.3906-2.44620.33594220.2765811798
2.4462-2.50740.32414030.2685821598
2.5074-2.57520.32343890.2676816398
2.5752-2.6510.3354540.2759818598
2.651-2.73650.3044180.2677819598
2.7365-2.83430.32884530.2711820398
2.8343-2.94770.31274710.268816098
2.9477-3.08180.32034390.2664815598
3.0818-3.24430.29784420.2544822098
3.2443-3.44740.28984690.2483818998
3.4474-3.71340.27524340.2357817998
3.7134-4.08680.27024450.2275811098
4.0868-4.67740.23574040.211813797
4.6774-5.89010.24254420.212812797
5.8901-40.440.2364480.193806497

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