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- PDB-4nna: Apo structure of ObcA -

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Basic information

Entry
Database: PDB / ID: 4nna
TitleApo structure of ObcA
ComponentsOBCA, Oxalate Biosynthetic Component A
KeywordsLYASE / alpha/beta barrel protein / oxlate biosynthase / Methylation / Seleno-Met labeling
Function / homology
Function and homology information


3-keto-5-aminohexanoate cleavage activity / metal ion binding
Similarity search - Function
: / Oxalate Biosynthetic Component A, N-terminal domain / 3-keto-5-aminohexanoate cleavage enzyme / beta-keto acid cleavage enzyme / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Oxalate Biosynthetic Component A N-terminal domain-containing protein
Similarity search - Component
Biological speciesBurkholderia glumae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.103 Å
AuthorsOh, J.T. / Goo, E. / Hwang, I. / Rhee, S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis for Bacterial Quorum Sensing-mediated Oxalogenesis.
Authors: Oh, J. / Goo, E. / Hwang, I. / Rhee, S.
History
DepositionNov 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2May 7, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OBCA, Oxalate Biosynthetic Component A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8772
Polymers59,8531
Non-polymers241
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)173.548, 173.548, 46.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1054-

HOH

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Components

#1: Protein OBCA, Oxalate Biosynthetic Component A


Mass: 59853.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia glumae (bacteria) / Strain: BGR1 / Gene: bglu_2g18790 / Production host: Escherichia coli (E. coli)
References: UniProt: C5AJX5, Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris pH 8.0, 0.2M magnesium chloride, 20% PEG6000 , VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 7A (6B, 6C1)10.97935
SYNCHROTRONPAL/PLS 7A (6B, 6C1)20.97951
SYNCHROTRONPAL/PLS 7A (6B, 6C1)30.97167
DetectorType: ADSC Quantum Q270r / Detector: CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
3MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.979511
30.971671
ReflectionResolution: 2.1→50 Å / Num. obs: 40015 / % possible obs: 95.9 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 12.13
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 5.02 / % possible all: 99.75

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.103→38.807 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 20.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 2000 5 %
Rwork0.1978 --
obs0.1998 40014 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.103→38.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3867 0 1 402 4270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073950
X-RAY DIFFRACTIONf_angle_d1.0775371
X-RAY DIFFRACTIONf_dihedral_angle_d14.8611463
X-RAY DIFFRACTIONf_chiral_restr0.068604
X-RAY DIFFRACTIONf_plane_restr0.005703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1029-2.15550.23151440.1932725X-RAY DIFFRACTION100
2.1555-2.21380.25831480.18862814X-RAY DIFFRACTION100
2.2138-2.27890.26651450.19522773X-RAY DIFFRACTION100
2.2789-2.35250.27821470.19322786X-RAY DIFFRACTION100
2.3525-2.43650.26221480.18672806X-RAY DIFFRACTION100
2.4365-2.53410.23511460.19712776X-RAY DIFFRACTION100
2.5341-2.64940.25221470.19712805X-RAY DIFFRACTION100
2.6494-2.7890.23981480.20092810X-RAY DIFFRACTION100
2.789-2.96370.23761480.19062811X-RAY DIFFRACTION100
2.9637-3.19240.22871470.19242790X-RAY DIFFRACTION99
3.1924-3.51350.19431440.19252740X-RAY DIFFRACTION96
3.5135-4.02150.23181320.18882517X-RAY DIFFRACTION88
4.0215-5.06480.23571170.18662222X-RAY DIFFRACTION77
5.0648-38.81310.2441390.23622639X-RAY DIFFRACTION86

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