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- PDB-4nnb: Binary complex of ObcA with oxaloacetate -

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Basic information

Entry
Database: PDB / ID: 4nnb
TitleBinary complex of ObcA with oxaloacetate
ComponentsOBCA, Oxalate Biosynthetic Component A
KeywordsLYASE / alpha/beta barrel protein / oxlate biosynthase
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
OXALOACETATE ION / Oxalate Biosynthetic Component A N-terminal domain-containing protein
Similarity search - Component
Biological speciesBurkholderia glumae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)59,5453
Polymers59,3901
Non-polymers1552
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)177.005, 177.005, 47.833
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-983-

HOH

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Components

#1: Protein OBCA, Oxalate Biosynthetic Component A


Mass: 59389.566 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: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 3% PEG 400, 2.08M Ammonium Sulfate, 0.1M Magnesium Chlorite, 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97935 Å
DetectorType: ADSC Quantum Q270r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 49954 / % possible obs: 96.15 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 13.29
Reflection shellResolution: 2→2.07 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4.73 / % possible all: 99.96

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.58 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 2000 4 %
Rwork0.2104 --
obs0.2117 49951 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 10 305 4056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073827
X-RAY DIFFRACTIONf_angle_d1.0895200
X-RAY DIFFRACTIONf_dihedral_angle_d15.5161415
X-RAY DIFFRACTIONf_chiral_restr0.072588
X-RAY DIFFRACTIONf_plane_restr0.005684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.29231440.23863465X-RAY DIFFRACTION100
2.05-2.10540.25951480.22793514X-RAY DIFFRACTION100
2.1054-2.16740.22511450.21153518X-RAY DIFFRACTION100
2.1674-2.23730.28531470.20853496X-RAY DIFFRACTION100
2.2373-2.31730.24871450.20833491X-RAY DIFFRACTION100
2.3173-2.41010.25311470.20883510X-RAY DIFFRACTION100
2.4101-2.51970.24791470.20433524X-RAY DIFFRACTION100
2.5197-2.65260.29051470.20973538X-RAY DIFFRACTION100
2.6526-2.81870.24481460.21053511X-RAY DIFFRACTION99
2.8187-3.03630.23281480.21043523X-RAY DIFFRACTION99
3.0363-3.34170.23061460.21113514X-RAY DIFFRACTION98
3.3417-3.82490.2411390.19623325X-RAY DIFFRACTION93
3.8249-4.81760.19311210.19452904X-RAY DIFFRACTION79
4.8176-39.58730.28731300.23443118X-RAY DIFFRACTION81

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