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- PDB-5exe: Crystal structure of oxalate oxidoreductase from Moorella thermoa... -

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Basic information

Entry
Database: PDB / ID: 5exe
TitleCrystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-TPP adduct
Components(Oxalate oxidoreductase subunit ...) x 3
KeywordsOXIDOREDUCTASE / oxalate / OFOR / thiamine
Function / homology
Function and homology information


oxalate oxidoreductase / oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / oxalate catabolic process / thiamine pyrophosphate binding / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate / : / Pyruvate:ferredoxin oxidoreductase, core domain II / Pyruvate:ferredoxin oxidoreductase core domain II / Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain / : / Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg / Pyruvate-flavodoxin oxidoreductase, central domain / Pyruvate/ketoisovalerate oxidoreductase, catalytic domain / Pyruvate ferredoxin/flavodoxin oxidoreductase ...2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate / : / Pyruvate:ferredoxin oxidoreductase, core domain II / Pyruvate:ferredoxin oxidoreductase core domain II / Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain / : / Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg / Pyruvate-flavodoxin oxidoreductase, central domain / Pyruvate/ketoisovalerate oxidoreductase, catalytic domain / Pyruvate ferredoxin/flavodoxin oxidoreductase / Rossmann fold - #920 / 4Fe-4S binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5SR / IRON/SULFUR CLUSTER / Oxalate oxidoreductase subunit delta / Oxalate oxidoreductase subunit alpha / Oxalate oxidoreductase subunit beta
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsGibson, M.I. / Chen, P.Y.-T. / Drennan, C.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography.
Authors: Gibson, M.I. / Chen, P.Y. / Johnson, A.C. / Pierce, E. / Can, M. / Ragsdale, S.W. / Drennan, C.L.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Data collection
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxalate oxidoreductase subunit alpha
B: Oxalate oxidoreductase subunit delta
C: Oxalate oxidoreductase subunit beta
D: Oxalate oxidoreductase subunit alpha
E: Oxalate oxidoreductase subunit delta
F: Oxalate oxidoreductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,09418
Polymers223,9526
Non-polymers3,14212
Water43,8122432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36130 Å2
ΔGint-337 kcal/mol
Surface area58460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.653, 144.131, 161.715
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Oxalate oxidoreductase subunit ... , 3 types, 6 molecules ADBECF

#1: Protein Oxalate oxidoreductase subunit alpha / OOR subunit alpha


Mass: 43737.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Moorella thermoacetica (strain ATCC 39073) (bacteria)
Strain: ATCC 39073 / References: UniProt: Q2RI41, oxalate oxidoreductase
#2: Protein Oxalate oxidoreductase subunit delta / OOR delta subunit


Mass: 33960.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Moorella thermoacetica (strain ATCC 39073) (bacteria)
Strain: ATCC 39073 / References: UniProt: Q2RI40, oxalate oxidoreductase
#3: Protein Oxalate oxidoreductase subunit beta / OOR subunit beta


Mass: 34277.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Moorella thermoacetica (strain ATCC 39073) (bacteria)
Strain: ATCC 39073 / References: UniProt: Q2RI42, oxalate oxidoreductase

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Non-polymers , 5 types, 2444 molecules

#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-5SR / [2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-carboxy-4-methyl-1,3-thiazol-3-ium-5-yl]ethoxy-oxidanyl-phosphoryl] hydrogen phosphate


Mass: 468.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18N4O9P2S
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2432 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystals were grown in a Coy anaerobic chamber under an Ar/H2 gas mixture. OOR was mixed with the well solution containing PEG 3000 and Tacsimate (pH 7.0), in drops composed of 1 uL well ...Details: Crystals were grown in a Coy anaerobic chamber under an Ar/H2 gas mixture. OOR was mixed with the well solution containing PEG 3000 and Tacsimate (pH 7.0), in drops composed of 1 uL well solution and 1 uL OOR (30 mg/ml) with the addition of 0.2 uL of 100 mM oxalic acid (pH 8.0) to the crystallization drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 200377 / % possible obs: 94.4 % / Redundancy: 5.9 % / Rsym value: 0.129 / Net I/σ(I): 7.7
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 1.9 / % possible all: 75

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
Cootmodel building
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C4I

5c4i


Resolution: 1.88→48.704 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2126 10067 5.03 %
Rwork0.1814 --
obs0.183 200261 92.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→48.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15461 0 110 2432 18003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616341
X-RAY DIFFRACTIONf_angle_d1.00222254
X-RAY DIFFRACTIONf_dihedral_angle_d13.4966040
X-RAY DIFFRACTIONf_chiral_restr0.0362436
X-RAY DIFFRACTIONf_plane_restr0.0062895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8786-1.89990.33871570.28823003X-RAY DIFFRACTION44
1.8999-1.92230.32812740.31065030X-RAY DIFFRACTION75
1.9223-1.94570.31512720.29185252X-RAY DIFFRACTION78
1.9457-1.97030.28962720.28865391X-RAY DIFFRACTION79
1.9703-1.99630.28932920.28715526X-RAY DIFFRACTION82
1.9963-2.02360.322850.27535669X-RAY DIFFRACTION83
2.0236-2.05250.29943110.26515773X-RAY DIFFRACTION86
2.0525-2.08320.28613440.25346050X-RAY DIFFRACTION89
2.0832-2.11570.29383090.2536299X-RAY DIFFRACTION93
2.1157-2.15040.2633450.24216523X-RAY DIFFRACTION96
2.1504-2.18750.25633480.23136649X-RAY DIFFRACTION98
2.1875-2.22730.26333790.22756666X-RAY DIFFRACTION99
2.2273-2.27010.26163720.21446713X-RAY DIFFRACTION99
2.2701-2.31640.25153660.20696741X-RAY DIFFRACTION100
2.3164-2.36680.23883240.19476767X-RAY DIFFRACTION99
2.3668-2.42180.22563570.1876762X-RAY DIFFRACTION99
2.4218-2.48240.22383530.1886671X-RAY DIFFRACTION98
2.4824-2.54950.24083960.1856634X-RAY DIFFRACTION98
2.5495-2.62450.21273900.17496765X-RAY DIFFRACTION99
2.6245-2.70920.21093650.17416787X-RAY DIFFRACTION100
2.7092-2.80610.21213430.17556778X-RAY DIFFRACTION100
2.8061-2.91840.20063480.176828X-RAY DIFFRACTION100
2.9184-3.05120.21223490.17116860X-RAY DIFFRACTION100
3.0512-3.2120.18963580.16456728X-RAY DIFFRACTION98
3.212-3.41320.20243090.16086786X-RAY DIFFRACTION98
3.4132-3.67670.17933800.15416842X-RAY DIFFRACTION99
3.6767-4.04650.16983760.13646853X-RAY DIFFRACTION100
4.0465-4.63170.16313640.12946887X-RAY DIFFRACTION99
4.6317-5.83390.15653520.14226848X-RAY DIFFRACTION98
5.8339-48.72080.19173770.17477113X-RAY DIFFRACTION98

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