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

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Basic information

Entry
Database: PDB / ID: 5exd
TitleCrystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-di-oxido-methyl-TPP (COOM-TPP) intermediate
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 / response to oxidative stress / metal ion binding
Similarity search - Function
: / : / : / 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate / : / Pyruvate-ferredoxin Oxidoreductase; domain 3 / Pyruvate-ferredoxin oxidoreductase, PFOR, domain III / Pyruvate:ferredoxin oxidoreductase, core domain II / Pyruvate:ferredoxin oxidoreductase core domain II / Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain ...: / : / : / 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate / : / Pyruvate-ferredoxin Oxidoreductase; domain 3 / Pyruvate-ferredoxin oxidoreductase, PFOR, domain III / 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 / Alpha-Beta Plaits - #20 / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-O2T / IRON/SULFUR CLUSTER / THIAMINE DIPHOSPHATE / 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: 2.5 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_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_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
G: Oxalate oxidoreductase subunit alpha
H: Oxalate oxidoreductase subunit delta
I: Oxalate oxidoreductase subunit beta
J: Oxalate oxidoreductase subunit alpha
K: Oxalate oxidoreductase subunit delta
L: Oxalate oxidoreductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)454,01132
Polymers447,90412
Non-polymers6,10720
Water30617
1
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)227,05016
Polymers223,9526
Non-polymers3,09810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35850 Å2
ΔGint-340 kcal/mol
Surface area57910 Å2
MethodPISA
2
G: Oxalate oxidoreductase subunit alpha
H: Oxalate oxidoreductase subunit delta
I: Oxalate oxidoreductase subunit beta
J: Oxalate oxidoreductase subunit alpha
K: Oxalate oxidoreductase subunit delta
L: Oxalate oxidoreductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,96116
Polymers223,9526
Non-polymers3,00910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35560 Å2
ΔGint-347 kcal/mol
Surface area58140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.430, 138.430, 217.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Oxalate oxidoreductase subunit ... , 3 types, 12 molecules ADGJBEHKCFIL

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


Mass: 43737.645 Da / Num. of mol.: 4 / 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.: 4 / 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.: 4 / 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, 37 molecules

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


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-O2T / [2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-[1,1,2-tris(oxidanyl)-2-oxidanylidene-ethyl]-1,3-thiazol-3-ium-5-yl]ethoxy-oxidanyl-phosphoryl] hydrogen phosphate


Mass: 514.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N4O11P2S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
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).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.64
ReflectionResolution: 2.5→50 Å / Num. obs: 131808 / % possible obs: 93.2 % / Redundancy: 4.7 % / Rsym value: 0.183 / Net I/σ(I): 6.8
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 1.9 / % possible all: 64.5

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Processing

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

5c4i


Resolution: 2.5→48.942 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 32.91 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2288 6653 5.05 %
Rwork0.1956 --
obs0.2066 131805 93.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30365 0 210 17 30592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331376
X-RAY DIFFRACTIONf_angle_d0.7142736
X-RAY DIFFRACTIONf_dihedral_angle_d11.24111488
X-RAY DIFFRACTIONf_chiral_restr0.0294700
X-RAY DIFFRACTIONf_plane_restr0.0045544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4959-2.53890.31342450.28114340X-RAY DIFFRACTION62
2.5389-2.58510.29092630.27244883X-RAY DIFFRACTION69
2.5851-2.63480.28772970.27385394X-RAY DIFFRACTION77
2.6348-2.68850.30043050.28435884X-RAY DIFFRACTION83
2.6885-2.74690.30613320.27166108X-RAY DIFFRACTION87
2.7469-2.81080.30063880.26816220X-RAY DIFFRACTION88
2.8108-2.8810.30683510.26346347X-RAY DIFFRACTION90
2.881-2.95890.26953290.25566494X-RAY DIFFRACTION92
2.9589-3.04590.27023220.25056591X-RAY DIFFRACTION94
3.0459-3.14410.2833480.2416650X-RAY DIFFRACTION93
3.1441-3.25630.28943530.23666640X-RAY DIFFRACTION94
3.2563-3.38660.27163330.23316637X-RAY DIFFRACTION95
3.3866-3.54050.24773670.21956611X-RAY DIFFRACTION94
3.5405-3.72680.23443290.19736675X-RAY DIFFRACTION94
3.7268-3.95990.21693180.17976601X-RAY DIFFRACTION93
3.9599-4.26490.19053180.16786615X-RAY DIFFRACTION94
4.2649-4.69280.18163170.15666654X-RAY DIFFRACTION94
4.6928-5.36870.1643320.15066621X-RAY DIFFRACTION94
5.3687-6.75230.16333270.16246605X-RAY DIFFRACTION93
6.7523-30.82760.18973660.15726600X-RAY DIFFRACTION92

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