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- PDB-6n2o: 2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marin... -

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Basic information

Entry
Database: PDB / ID: 6n2o
Title2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus with 2-oxoglutarate, coenzyme A and succinyl-CoA bound
Components
  • Pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit
  • Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein
KeywordsOXIDOREDUCTASE / thiamine pyrophosphate / [4Fe-4S] cluster / carbon fixation / reductive tricarboxylic acid cycle / rTCA / 2-oxoglutarate:ferredoxin oxidoreductase / electron transfer
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors / thiamine pyrophosphate binding / catalytic activity
Similarity search - Function
2-oxoacid:acceptor oxidoreductase, beta subunit / Pyruvate ferredoxin oxidoreductase beta subunit, C-terminal / Pyruvate ferredoxin oxidoreductase beta subunit C terminal / 2-oxoacid:acceptor oxidoreductase, alpha subunit / 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 ...2-oxoacid:acceptor oxidoreductase, beta subunit / Pyruvate ferredoxin oxidoreductase beta subunit, C-terminal / Pyruvate ferredoxin oxidoreductase beta subunit C terminal / 2-oxoacid:acceptor oxidoreductase, alpha subunit / 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 / 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-binding fold
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / COENZYME A / SUCCINYL-COENZYME A / IRON/SULFUR CLUSTER / THIAMINE DIPHOSPHATE / Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein / Pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit
Similarity search - Component
Biological speciesMagnetococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.824 Å
AuthorsChen, P.Y.-T. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126982 United States
CitationJournal: Joule / Year: 2019
Title: A reverse TCA cycle 2-oxoacid:ferredoxin oxidoreductase that makes C-C bonds from CO2.
Authors: Chen, P.Y. / Li, B. / Drennan, C.L. / Elliott, S.J.
History
DepositionNov 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein
B: Pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit
C: Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein
D: Pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,11613
Polymers187,7324
Non-polymers3,3849
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26190 Å2
ΔGint-222 kcal/mol
Surface area52720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.407, 100.532, 202.053
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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Protein , 2 types, 4 molecules ACBD

#1: Protein Pyruvate flavodoxin/ferredoxin oxidoreductase domain protein


Mass: 62159.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1) (bacteria)
Strain: ATCC BAA-1437 / JCM 17883 / MC-1 / Gene: Mmc1_1749 / Production host: Escherichia coli (E. coli) / References: UniProt: A0L8G4
#2: Protein Pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit


Mass: 31706.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1) (bacteria)
Strain: ATCC BAA-1437 / JCM 17883 / MC-1 / Gene: Mmc1_1750 / Production host: Escherichia coli (E. coli) / References: UniProt: A0L8G5

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Non-polymers , 7 types, 31 molecules

#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-SCA / SUCCINYL-COENZYME A / Succinyl-CoA


Mass: 867.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 27% (w/v) PEG 4000 and 0.08 M sodium cacodylate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 38629 / % possible obs: 90.7 % / Redundancy: 8.1 % / Rsym value: 0.133 / Net I/σ(I): 10.9
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 2935 / CC1/2: 0.857

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N2N

6n2n


Resolution: 2.824→90.006 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.8
RfactorNum. reflection% reflection
Rfree0.2605 1929 5 %
Rwork0.2124 --
obs0.2148 38579 89.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.824→90.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13019 0 183 22 13224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313534
X-RAY DIFFRACTIONf_angle_d0.58318357
X-RAY DIFFRACTIONf_dihedral_angle_d14.5178053
X-RAY DIFFRACTIONf_chiral_restr0.0451987
X-RAY DIFFRACTIONf_plane_restr0.0042384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8239-2.89450.3966800.32081519X-RAY DIFFRACTION52
2.8945-2.97280.3891160.30652195X-RAY DIFFRACTION76
2.9728-3.06030.36311250.29152372X-RAY DIFFRACTION83
3.0603-3.1590.29881310.27862504X-RAY DIFFRACTION87
3.159-3.2720.30651390.28542651X-RAY DIFFRACTION92
3.272-3.4030.34241460.26622748X-RAY DIFFRACTION95
3.403-3.55790.3081470.25972789X-RAY DIFFRACTION96
3.5579-3.74540.29111470.23682807X-RAY DIFFRACTION97
3.7454-3.98010.29421480.2242816X-RAY DIFFRACTION97
3.9801-4.28740.24331500.19862837X-RAY DIFFRACTION97
4.2874-4.71880.2441480.18042830X-RAY DIFFRACTION97
4.7188-5.40160.21211500.17542830X-RAY DIFFRACTION96
5.4016-6.80510.22371490.18582844X-RAY DIFFRACTION95
6.8051-90.05220.19671530.16272908X-RAY DIFFRACTION93

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