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- PDB-1kek: Crystal Structure of the Free Radical Intermediate of Pyruvate:Fe... -

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Basic information

Entry
Database: PDB / ID: 1kek
TitleCrystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase
ComponentsPyruvate-Ferredoxin OxidoreductasePyruvate synthase
KeywordsOXIDOREDUCTASE / homodimer / 7 domains
Function / homology
Function and homology information


pyruvate synthase / pyruvate synthase activity / thiamine pyrophosphate binding / electron transport chain / 4 iron, 4 sulfur cluster binding / 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; domain 3 / Pyruvate-ferredoxin oxidoreductase, PFOR, domain III / 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; domain 3 / Pyruvate-ferredoxin oxidoreductase, PFOR, domain III / 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, 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 / Alpha-Beta Plaits - #20 / 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
CARBON DIOXIDE / 2-ACETYL-THIAMINE DIPHOSPHATE / IRON/SULFUR CLUSTER / Pyruvate:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesDesulfovibrio africanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChabriere, E. / Vernede, X. / Guigliarelli, B. / Charon, M.-H. / Hatchikian, E.C. / Fontecilla-Camps, J.C.
CitationJournal: 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
DepositionNov 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate-Ferredoxin Oxidoreductase
B: Pyruvate-Ferredoxin Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,66916
Polymers267,4082
Non-polymers3,26114
Water34,1021893
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31700 Å2
ΔGint-291 kcal/mol
Surface area74720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.110, 145.760, 210.260
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 / Pyruvate synthase


Mass: 133703.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio africanus (bacteria) / References: UniProt: P94692, pyruvate synthase

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Non-polymers , 6 types, 1907 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-HTL / 2-ACETYL-THIAMINE DIPHOSPHATE / 2-ACETYL-3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-4-METHYL-5-(4,6,6-TRIHYDROXY-3,5-DIOXA-4,6-DIPHOSPHAHEX-1-YL)THIAZOLIUM INNER SALT P,P'-DIOXIDE


Mass: 467.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21N4O8P2S
#6: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1893 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 6000 10-15%, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Chabriere, E., (1999) Nat.Struct.Biol., 6, 182.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 1.005 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 7, 1998
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 1.9→27.38 Å / Num. all: 216598 / Num. obs: 216598 / % possible obs: 94.4 % / Observed criterion σ(F): 11.6 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.084
Reflection shellResolution: 1.87→1.97 Å / Mean I/σ(I) obs: 1.4 / Rsym value: 0.293 / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 1.87 Å / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.293

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLORrefinement
REFMACrefinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.38 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3963562.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: X-PLOR + Home dictionary
Details: THIS REFINED SET DIFFERS SLIGHTLY FROM THE ONE REPORTED IN REF. FOR EXAMPLE, THE C2ALPHA-C2 DISTANCES OF THE RADICAL SPECIES DO NOT MATCH EXACTLY THE PUBLISHED ONES.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 10008 4.9 %RANDOM
Rwork0.178 ---
all0.178 210949 --
obs0.178 210949 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 79.3491 Å2 / ksol: 0.38557 e/Å3
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.53 Å20 Å20 Å2
2--1.34 Å20 Å2
3---3.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18766 0 116 1893 20775
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg2.9
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d2.87
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 1525 4.9 %
Rwork0.263 29881 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARA.INPTOPO.INP
Software
*PLUS
Name: 'XPLOR, REFMAC' / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.87 Å / Lowest resolution: 30 Å / Num. reflection obs: 200561 / σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.183 / Rfactor Rfree: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0014
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d

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