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- PDB-5ikz: Glycerol bound structure of Obc1, a bifunctional enzyme for quoru... -

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Basic information

Entry
Database: PDB / ID: 5ikz
TitleGlycerol bound structure of Obc1, a bifunctional enzyme for quorum sensing-dependent oxalogenesis
ComponentsOxalate biosynthetic component 1
KeywordsHYDROLASE / LYASE / alpha / beta hydrolase
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / :
Function and homology information
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsOh, J. / Rhee, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Rural Development Administration, Plant Molecular Breeding CenterPJ01101901 Korea, Republic Of
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Insights into an Oxalate-producing Serine Hydrolase with an Unusual Oxyanion Hole and Additional Lyase Activity
Authors: Oh, J. / Hwang, I. / Rhee, S.
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxalate biosynthetic component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,5343
Polymers124,4171
Non-polymers1162
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area41840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.970, 229.970, 253.763
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1380-

HOH

21A-1438-

HOH

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Components

#1: Protein Oxalate biosynthetic component 1


Mass: 124417.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301) (bacteria)
Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: DR63_4704 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A096YSN3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 5.23 Å3/Da / Density % sol: 76.47 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES pH 7.0, 1M Sodium citrate tribasic / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→78.34 Å / Num. obs: 63296 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 56.96 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.277 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.8717.52.6471100
12.83-78.3418.50.07198.2

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimless0.5.12data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IKY

5iky


Resolution: 2.8→46.349 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.32
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2274 3166 5 %
Rwork0.1985 --
obs0.2 63263 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 167.91 Å2 / Biso mean: 69.4751 Å2 / Biso min: 28.62 Å2
Refinement stepCycle: final / Resolution: 2.8→46.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7848 0 7 207 8062
Biso mean--79.66 54.79 -
Num. residues----1047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038030
X-RAY DIFFRACTIONf_angle_d0.6910978
X-RAY DIFFRACTIONf_chiral_restr0.0261274
X-RAY DIFFRACTIONf_plane_restr0.0031440
X-RAY DIFFRACTIONf_dihedral_angle_d12.1012818
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.84180.34691310.312726052736100
2.8418-2.88620.32891330.291525672700100
2.8862-2.93350.30571450.282225962741100
2.9335-2.98410.32711540.281225832737100
2.9841-3.03840.30191710.272725552726100
3.0384-3.09680.30641280.26825972725100
3.0968-3.160.27751220.253926182740100
3.16-3.22870.25111380.235125862724100
3.2287-3.30380.25881290.231126152744100
3.3038-3.38640.2741160.224326272743100
3.3864-3.47790.24931380.211426032741100
3.4779-3.58020.23961450.202425932738100
3.5802-3.69570.21571340.200525902724100
3.6957-3.82780.23191740.194225872761100
3.8278-3.98090.24141450.175726102755100
3.9809-4.1620.1941320.171326162748100
4.162-4.38130.17951210.156326412762100
4.3813-4.65550.17461420.149525882730100
4.6555-5.01460.19131380.152626212759100
5.0146-5.51850.18471300.168926522782100
5.5185-6.31530.24061140.199526752789100
6.3153-7.95010.20071400.205126652805100
7.9501-46.35540.2051460.18122707285399
Refinement TLS params.Method: refined / Origin x: 14.049 Å / Origin y: -36.561 Å / Origin z: 27.1331 Å
111213212223313233
T0.4828 Å20.0277 Å2-0.1081 Å2-0.3822 Å20.0972 Å2--0.3755 Å2
L0.8896 °20.1806 °20.0072 °2-1.0933 °2-0.1137 °2--0.6827 °2
S-0.0653 Å °-0.1341 Å °-0.1047 Å °0.1122 Å °0.0925 Å °-0.1657 Å °0.1466 Å °0.2366 Å °0.0231 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 1106
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 207
4X-RAY DIFFRACTION1allC1

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