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- PDB-2pda: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PYRUVATE-FERREDOXIN OXID... -

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Basic information

Entry
Database: PDB / ID: 2pda
TitleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS AND PYRUVATE.
ComponentsPROTEIN (PYRUVATE-FERREDOXIN OXIDOREDUCTASE)
KeywordsOXIDOREDUCTASE / PYRUVATE CATABOLISM / IRON-SULFUR CLUSTER / TPP-DEPENDENT ENZYME / COMPLEX
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 / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Alpha-Beta Plaits - #20 / 4Fe-4S binding domain / 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
PYRUVIC ACID / IRON/SULFUR CLUSTER / THIAMINE DIPHOSPHATE / Pyruvate:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesDesulfovibrio africanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChabriere, E. / Charon, M.H.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate.
Authors: Chabriere, E. / Charon, M.H. / Volbeda, A. / Pieulle, L. / Hatchikian, E.C. / Fontecilla-Camps, J.C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary Crystallographic Analysis of the Pyruvate- Ferredoxin Oxidoreductase from Desulfovibrio Africanus
Authors: Pieulle, L. / Chabriere, E. / Hatchikian, E.C. / Fontecilla-Camps, J.F. / Charon, M.H.
History
DepositionNov 10, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 23, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
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 / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PYRUVATE-FERREDOXIN OXIDOREDUCTASE)
B: PROTEIN (PYRUVATE-FERREDOXIN OXIDOREDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,67316
Polymers267,4082
Non-polymers3,26514
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31340 Å2
ΔGint-288 kcal/mol
Surface area74850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.000, 146.300, 211.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.995625, 0.04342, -0.08274), (0.041889, -0.584115, -0.812509), (-0.083525, -0.810509, 0.579741)
Vector: -39.023, -68.059, -36.976)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 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, PYRUVIC ACID
Source: (natural) Desulfovibrio africanus (bacteria) / Cellular location: CYTOPLASM / Strain: NCIB 8401 / References: UniProt: P94692, pyruvate synthase

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Non-polymers , 6 types, 28 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


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


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#6: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.34 Å3/Da / Density % sol: 50.63 %
Crystal growpH: 6.2
Details: PEG6000 11% MGCL2 100MM CACODYLATE 100MM PH 6.2 PYRUVATE 100MM
Crystal
*PLUS
Density % sol: 54 %
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: Pieulle, L., (1999) Acta Crystallogr., Sect.D, 55, 329.
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1droppH8.5
212-15 %PEG60001reservoir
3100 mM1reservoircan be replaced by 10mM BaCl2. CaCl2, CoCl2 or MnCl2.MgCl2
4100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.997
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 50700 / % possible obs: 94.2 % / Redundancy: 2.6 % / Biso Wilson estimate: 33.65 Å2 / Rsym value: 0.098 / Net I/σ(I): 6.9
Reflection shellResolution: 3→3.16 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.179 / % possible all: 96.1
Reflection
*PLUS
Rmerge(I) obs: 0.098
Reflection shell
*PLUS
Highest resolution: 3 Å / % possible obs: 96.1 % / Rmerge(I) obs: 0.179

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
X-PLORmodel building
X-PLOR3.854refinement
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→10 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.297 2475 5 %RANDOM
Rwork0.234 ---
obs-49492 94.2 %-
Displacement parametersBiso mean: 12.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.3 Å2--
2--2.45 Å2-
3----8.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-4 Å
Luzzati sigma a0.76 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18764 0 116 14 18894
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.21
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.76
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.61.5
X-RAY DIFFRACTIONx_mcangle_it1.052
X-RAY DIFFRACTIONx_scbond_it0.822
X-RAY DIFFRACTIONx_scangle_it1.322.5
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 3→3.13 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.384 316 5 %
Rwork0.2997 5900 -
obs--96.1 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.854 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 12.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.21
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.76
X-RAY DIFFRACTIONx_mcbond_it0.61.5
X-RAY DIFFRACTIONx_scbond_it0.822
X-RAY DIFFRACTIONx_mcangle_it1.052
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 3 Å / Rfactor Rfree: 0.384 / % reflection Rfree: 5 %

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