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- PDB-1l3j: Crystal Structure of Oxalate Decarboxylase Formate Complex -

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Basic information

Entry
Database: PDB / ID: 1l3j
TitleCrystal Structure of Oxalate Decarboxylase Formate Complex
ComponentsYVRK PROTEIN
KeywordsMETAL BINDING PROTEIN / OXALATE / DECARBOXYLASE / FORMATE / MANGANESE / CUPIN
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _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

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Assembly

Deposited unit
A: YVRK PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8476
Polymers43,6211
Non-polymers2265
Water6,918384
1
A: YVRK PROTEIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)263,08336
Polymers261,7256
Non-polymers1,35730
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 area48340 Å2
ΔGint-399 kcal/mol
Surface area68360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)154.800, 154.800, 122.160
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 performing a three folds and a two fold symmetry operation on chain A

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Components

#1: Protein YVRK PROTEIN / oxalate decarboxylase


Mass: 43620.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yvrK / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / 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 / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: PEG 4000, formate,Tris, sodium chloride, pH 8.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.948 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 1.9→40.72 Å / Num. obs: 44171 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 5.8 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 7.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40.72 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4241187.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.193 4439 10 %RANDOM
Rwork0.169 ---
all0.182 ---
obs0.169 44171 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.6453 Å2 / ksol: 0.377357 e/Å3
Displacement parametersBiso mean: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.05 Å2-0.87 Å20 Å2
2---3.05 Å20 Å2
3---6.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.9→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 9 384 3363
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it2.812
X-RAY DIFFRACTIONc_scangle_it4.472.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.195 717 9.8 %
Rwork0.172 6594 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4FOR.PARAMFOR.TOP

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