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- PDB-1xlp: Structure of oxidized C73S putidaredoxin from Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 1xlp
TitleStructure of oxidized C73S putidaredoxin from Pseudomonas putida
ComponentsPutidaredoxin
KeywordsOXIDOREDUCTASE / [2Fe-2S] / ferredoxin
Function / homology
Function and homology information


P450-containing electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding / cytosol
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / 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) ...Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / 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 / Putidaredoxin
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / rigid body refinement / Resolution: 2 Å
AuthorsSevrioukova, I.F.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Redox-dependent structural reorganization in putidaredoxin, a vertebrate-type [2Fe-2S] ferredoxin from Pseudomonas putida.
Authors: Sevrioukova, I.F.
History
DepositionSep 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,7666
Polymers34,2393
Non-polymers5273
Water4,612256
1
A: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5892
Polymers11,4131
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5892
Polymers11,4131
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5892
Polymers11,4131
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Putidaredoxin
hetero molecules

C: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1774
Polymers22,8262
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_763-y+2,-x+1,-z-3/21
Buried area1890 Å2
ΔGint-45 kcal/mol
Surface area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.220, 66.220, 151.751
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-197-

HOH

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Components

#1: Protein Putidaredoxin / PDX


Mass: 11412.846 Da / Num. of mol.: 3 / Mutation: C73S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camB / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00259, EC: 1.9.3.2
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.3 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: lithium sulfate, sodium citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 2, 2004 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→34.36 Å / Num. all: 23647 / Num. obs: 23600 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 17
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2190 / Rsym value: 0.674 / % possible all: 98.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: rigid body refinement
Starting model: PDB entry 1oqr

1oqr


Resolution: 2→34.36 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1139 4.8 %random
Rwork0.217 ---
all0.217 23633 --
obs0.217 23600 99.9 %-
Solvent computationSolvent model: Flat Model / Bsol: 46.6 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 22.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→34.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 12 256 2649
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2→2.03 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.291 42 4.2 %
Rwork0.283 2190 -
obs-960 98.9 %

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