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- PDB-1j58: Crystal Structure of Oxalate Decarboxylase -

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Basic information

Entry
Database: PDB / ID: 1j58
TitleCrystal Structure of Oxalate Decarboxylase
ComponentsYVRK PROTEIN
KeywordsMETAL BINDING PROTEIN / CUPIN / DECARBOXYKLASE / OXALATE / MANGANESE / FORMATE
Function / homology
Function and homology information


oxalate decarboxylase / oxalate decarboxylase activity / oxalate metabolic process / 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
FORMIC ACID / : / Oxalate decarboxylase OxdC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsAnand, R. / Dorrestein, P.C. / Kinsland, C. / Begley, T.P. / Ealick, S.E.
CitationJournal: 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.
History
DepositionFeb 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: 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_sheet / 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.pdbx_leaving_atom_flag / _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 / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YVRK PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2235
Polymers44,0431
Non-polymers1804
Water7,909439
1
A: YVRK PROTEIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)265,33930
Polymers264,2586
Non-polymers1,08124
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 operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area47160 Å2
ΔGint-387 kcal/mol
Surface area68380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)154.700, 154.700, 123.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a hexamer constructed by doing a three fold and a two fold symmetry operation on chain A

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Components

#1: Protein YVRK PROTEIN / Oxalate Decarboxylase


Mass: 44042.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PET16b / Production host: Bacteria (eubacteria) / References: UniProt: O34714
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: PEG 4000, Tris-Hcl, sodium chloride, pH 8.0, VAPOR DIFFUSION, temperature 298K
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13 mg/mlprotein1drop
26 %(w/w)PEG40001reservoir
3200 mMTris1reservoirpH8.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: .9791, 0.9794, 0.9641, 0.9807
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.96411
40.98071
ReflectionResolution: 1.75→29.83 Å / Num. all: 57048 / Num. obs: 57048 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.1
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.23 / % possible all: 99.7
Reflection
*PLUS
Num. obs: 57307 / % possible obs: 99.9 % / Redundancy: 7.1 % / Num. measured all: 406760 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
Lowest resolution: 1.84 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 1.75→29.83 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3802941.91 / Data cutoff high rms absF: 3802941.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4063 7.1 %random
Rwork0.176 ---
all0.192 57048 --
obs0.181 57048 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.7172 Å2 / ksol: 0.387726 e/Å3
Displacement parametersBiso mean: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å2-0.24 Å20 Å2
2---2.4 Å20 Å2
3---4.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.75→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 6 439 3415
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.241 666 7.1 %
Rwork0.228 8750 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3FOR.PARAMFOR.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 25 Å / Num. reflection obs: 57039 / % reflection Rfree: 10 % / Rfactor all: 0.192 / Rfactor obs: 0.181 / Rfactor Rfree: 0.1784 / Rfactor Rwork: 0.1831
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.241 / Rfactor Rwork: 0.228

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