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- PDB-1l5p: Crystal Structure of Trichomonas vaginalis Ferredoxin -

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Basic information

Entry
Database: PDB / ID: 1l5p
TitleCrystal Structure of Trichomonas vaginalis Ferredoxin
Componentsferredoxin
KeywordsOXIDOREDUCTASE / [2Fe-2S] cluster / electron transfer / iron-sulfur protein / metalloprotein
Function / homology
Function and homology information


hydrogenosome / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsCrossnoe, C.R. / Germanas, J.P. / Le Magueres, P. / Mustata, G. / Krause, K.L.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The crystal structure of Trichomonas vaginalis ferredoxin provides insight into metronidazole activation.
Authors: Crossnoe, C.R. / Germanas, J.P. / LeMagueres, P. / Mustata, G. / Krause, K.L.
History
DepositionMar 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ferredoxin
B: ferredoxin
C: ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9036
Polymers29,3763
Non-polymers5273
Water90150
1
A: ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9682
Polymers9,7921
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9682
Polymers9,7921
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9682
Polymers9,7921
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.400, 64.550, 133.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ferredoxin /


Mass: 9792.007 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: pET-3a-TvFd / Plasmid: pET-26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21149
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 8000, 0.2 M sodium acetate, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
119.0 mg/mlprotein1drop
225 %(w/v)PEG80001reservoir
30.2 Msodium acetate1reservoir
40.1 Msodium cacodylate1reservoirpH6.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11701
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 22, 1999
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
10.95 polarizationSINGLE WAVELENGTHMx-ray1
20.95 polarizationMADMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→33 Å / Num. obs: 15472 / % possible obs: 96 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.28 Å / % possible all: 81
Reflection
*PLUS
Lowest resolution: 33 Å / % possible obs: 96 % / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
SOLVEphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→33 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.315 1531 -random
Rwork0.248 ---
all-15472 --
obs-15012 96 %-
Displacement parametersBiso mean: 39 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 12 50 2105
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.136
LS refinement shellResolution: 2.2→2.3 Å
RfactorNum. reflection
Rfree0.37 162
Rwork0.343 -
obs-1460
Refinement
*PLUS
Lowest resolution: 100 Å / Rfactor Rfree: 0.315 / Rfactor Rwork: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / Rfactor Rwork: 0.343

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