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- PDB-2uya: DEL162-163 mutant of Bacillus subtilis Oxalate Decarboxylase OxdC -

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Basic information

Entry
Database: PDB / ID: 2uya
TitleDEL162-163 mutant of Bacillus subtilis Oxalate Decarboxylase OxdC
ComponentsOXALATE DECARBOXYLASE OXDC
KeywordsLYASE / CUPIN / FORMATE / OXALATE / MANGANESE / METAL BINDING PROTEIN / METAL-BINDING / DECARBOXYLASE / DEL162-163 MUTANT
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
: / Oxalate decarboxylase OxdC
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJust, V.J. / Burrell, M.R. / Bowater, L. / McRobbie, I. / Stevenson, C.E.M. / Lawson, D.M. / Bornemann, S.
CitationJournal: Biochem.J. / Year: 2007
Title: The Identity of the Active Site of Oxalate Decarboxylase and the Importance of the Stability of Active-Site Lid Conformations.
Authors: Just, V.J. / Burrell, M.R. / Bowater, L. / Mcrobbie, I. / Stevenson, C.E.M. / Lawson, D.M. / Bornemann, S.
History
DepositionApr 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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)43,7376
Polymers43,3781
Non-polymers3605
Water7,404411
1
A: OXALATE DECARBOXYLASE OXDC
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)262,42436
Polymers260,2666
Non-polymers2,15730
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
Buried area51480 Å2
ΔGint-355.9 kcal/mol
Surface area84080 Å2
MethodPQS
Unit cell
Length a, b, c (Å)154.857, 154.857, 123.274
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 1 molecules A

#1: Protein OXALATE DECARBOXYLASE OXDC


Mass: 43377.691 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-161,164-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Plasmid: PLB36 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34714, oxalate decarboxylase

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Non-polymers , 5 types, 416 molecules

#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsDEL162-163 MUTANT

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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 %
Description: STARTING PHASES WERE OBTAINED BY RIGID BODY REFINEMENT OF 1UW8
Crystal growpH: 8.5 / Details: 8-15% PEG 8000, 0.1 M TRIS PH8.5, 0-15% XYLITOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→58.93 Å / Num. obs: 38270 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.87 % / Biso Wilson estimate: 16.51 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 22.21
Reflection shellResolution: 2→2.02 Å / Redundancy: 6.99 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.55 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UW8

1uw8


Resolution: 2→58.93 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.054 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.166 1908 5.06 %RANDOM
Rwork0.129 ---
obs0.13 38269 99.8 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.349 Å2-0.174 Å20 Å2
2---0.349 Å20 Å2
3---0.523 Å2
Refinement stepCycle: LAST / Resolution: 2→58.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2983 0 17 411 3411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223077
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.954177
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03724.4150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60115497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1671515
X-RAY DIFFRACTIONr_chiral_restr0.0990.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023432
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.2493
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21440
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2308
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.161.52042
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57623026
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.61431342
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8694.51151
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 8.85→58.93 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.26 27
Rwork0.208 460

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