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- PDB-2c3u: Crystal Structure Of Pyruvate-Ferredoxin Oxidoreductase From Desu... -

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Basic information

Entry
Database: PDB / ID: 2c3u
TitleCrystal Structure Of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio africanus, Oxygen inhibited form
ComponentsPYRUVATE-FERREDOXIN OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / 4FE-4S / IRON / IRON-SULFUR / IRON-SULFUR CLUSTER / PYRUVATE CATABOLISM / TPP-DEPENDENT ENZYME / METAL-BINDING / ELECTRON TRANSPORT
Function / homology
Function and homology information


pyruvate synthase / pyruvate synthase activity / thiamine pyrophosphate binding / electron transport chain / 4 iron, 4 sulfur cluster binding / response to oxidative stress / iron ion binding / cytoplasm
Similarity search - Function
Pyruvate-ferredoxin Oxidoreductase; domain 4 / Pyruvate-flavodoxin oxidoreductase, EKR domain / Pyruvate-ferredoxin Oxidoreductase; domain 7 / Pyruvate-ferredoxin Oxidoreductase; domain 7 / : / Pyruvate-ferredoxin oxidoreductase, insertion domain / Pyruvate-flavodoxin oxidoreductase / Pyruvate-flavodoxin oxidoreductase, EKR domain / Pyruvate-flavodoxin oxidoreductase, EKR domain superfamily / Domain of unknown function ...Pyruvate-ferredoxin Oxidoreductase; domain 4 / Pyruvate-flavodoxin oxidoreductase, EKR domain / Pyruvate-ferredoxin Oxidoreductase; domain 7 / Pyruvate-ferredoxin Oxidoreductase; domain 7 / : / Pyruvate-ferredoxin oxidoreductase, insertion domain / Pyruvate-flavodoxin oxidoreductase / Pyruvate-flavodoxin oxidoreductase, EKR domain / Pyruvate-flavodoxin oxidoreductase, EKR domain superfamily / Domain of unknown function / Domain of unknown function / 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 / Alpha-Beta Plaits - #20 / 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 dicluster domain / 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 / Few Secondary Structures / Irregular / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2TP / PYRUVIC ACID / IRON/SULFUR CLUSTER / Pyruvate:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesDESULFOVIBRIO AFRICANUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsCavazza, C. / Contreras-Martel, C. / Pieulle, L. / Chabriere, E. / Hatchikian, E.C. / Fontecilla-Camps, J.C.
Citation
Journal: Structure / Year: 2006
Title: Flexibility of Thiamine Diphosphate Revealed by Kinetic Crystallographic Studies of the Reaction of Pyruvate-Ferredoxin Oxidoreductase with Pyruvate.
Authors: Cavazza, C. / Contreras-Martel, C. / Pieulle, L. / Chabriere, E. / Hatchikian, E.C. / Fontecilla-Camps, J.C.
#1: Journal: Science / Year: 2001
Title: Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase.
Authors: Chabriere, E. / Vernede, X. / Guigliarelli, B. / Charon, M.-H. / Hatchikian, E.C. / Fontecilla-Camps, J.C.
History
DepositionOct 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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.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
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
B: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,70516
Polymers267,4082
Non-polymers3,29714
Water13,727762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.176, 146.810, 212.860
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 , 1 types, 2 molecules AB

#1: Protein PYRUVATE-FERREDOXIN OXIDOREDUCTASE


Mass: 133703.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: COMPLEXED WITH IRON/SULFUR CLUSTER, THIAMIN DIPHOSPHATE. CRYSTAL SOAKED OVERNIGHT WITH PYRUVATE
Source: (natural) DESULFOVIBRIO AFRICANUS (bacteria) / References: UniProt: P94692, pyruvate synthase

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Non-polymers , 6 types, 776 molecules

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


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-2TP / 2-(3-{[4-(HYDROXYAMINO)-2-METHYLPYRIMIDIN-5-YL]METHYL}-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL)ETHYL TRIHYDROGEN DIPHOSPHATE


Mass: 441.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O8P2S
#4: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 49.32 %
Crystal growpH: 9 / Details: 10% PEG6000, 100MM MGCL2, 100MM TRIS-HCL PH 9

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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: Apr 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.32→55 Å / Num. obs: 112651 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 13.3 Å2 / Rsym value: 0.1 / Net I/σ(I): 11.63
Reflection shellResolution: 2.32→2.5 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.96 / Rsym value: 0.28 / % possible all: 90.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KEK

1kek


Resolution: 2.32→49.48 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3866757.12 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 5682 5 %RANDOM
Rwork0.187 ---
obs0.187 112651 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.3221 Å2 / ksol: 0.344666 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.27 Å20 Å20 Å2
2--0.21 Å20 Å2
3---4.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.32→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18766 0 118 762 19646
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.981.5
X-RAY DIFFRACTIONc_mcangle_it2.872
X-RAY DIFFRACTIONc_scbond_it3.372
X-RAY DIFFRACTIONc_scangle_it4.452.5
LS refinement shellResolution: 2.32→2.47 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 879 5.1 %
Rwork0.215 16462 -
obs--89.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARA_FES.PARTOPO_FES.TOP
X-RAY DIFFRACTION3OTP_PYR_TRS.PAROTP_PYR_TRS.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5WATER.PARAMWATER.TOP

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