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- PDB-1uw8: CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE -

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Basic information

Entry
Database: PDB / ID: 1uw8
TitleCRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE
ComponentsOXALATE DECARBOXYLASE OXDC
KeywordsLYASE / METAL BINDING PROTEIN / CUPIN / DECARBOXYLASE / OXALATE / MANGANESE / FORMATE
Function / homology
Function and homology information


oxalate decarboxylase / oxalate decarboxylase activity / oxalate metabolic process / outer membrane-bounded periplasmic space / metal ion binding / cytoplasm
Similarity search - Function
Bicupin, oxalate decarboxylase/oxidase / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Oxalate decarboxylase OxdC
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJust, V.J. / Stevenson, C.E.M. / Bowater, L. / Tanner, A. / Lawson, D.M. / Bornemann, S.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: A Closed Conformation of Bacillus Subtilis Oxalate Decarboxylase Oxdc Provides Evidence for the True Identity of the Active Site
Authors: Just, V.J. / Stevenson, C.E.M. / Bowater, L. / Tanner, A. / Lawson, D.M. / Bornemann, S.
#1: Journal: Biochemistry / Year: 2002
Title: Structure of Oxalate Decarboxylase from Bacillus Subtilis at 1.75 A Resolution
Authors: Anand, R. / Dorrestein, P.C. / Kinsland, C. / Begley, T.P. / Ealick, S.E.
#2: Journal: J.Biol.Chem. / Year: 2001
Title: Oxalate Decarboxylase Requires Manganese and Dioxygen for Activity
Authors: Tanner, A. / Bowater, L. / Fairhurst, S.A. / Bornemann, S.
History
DepositionFeb 2, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OXALATE DECARBOXYLASE OXDC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8534
Polymers43,6211
Non-polymers2323
Water7,242402
1
A: OXALATE DECARBOXYLASE OXDC
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)263,11824
Polymers261,7256
Non-polymers1,39218
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)154.663, 154.663, 122.822
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2328-

HOH

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Components

#1: Protein OXALATE DECARBOXYLASE OXDC / OXDC


Mass: 43620.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FORMERLY KNOWN AS YVRK / Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Plasmid: PAT1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34714, oxalate decarboxylase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: 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: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 291 K / pH: 8.5 / Details: 8% PEG 8000, TRIS-HCL PH8.5, 18 DEG C, pH 8.50
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
220 mMTris1droppH7.0
38 %PEG80001reservoir
4100 mMTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 21, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 38069 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 23.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 34.4
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 6.7 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Redundancy: 23.6 % / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 6.7

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J58

1j58


Resolution: 2→91.29 Å / SU B: 1.95 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.1583 1899 5 %RANDOM
Rwork0.12746 ---
obs0.129 36145 100 %-
Displacement parametersBiso mean: 16.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0.49 Å20 Å2
2---0.99 Å20 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 2→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 10 402 3412
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.158 / Rfactor Rwork: 0.127
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.013
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.409

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