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- PDB-1xlq: Crystal structure of reduced C73S putidaredoxin from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 1xlq
TitleCrystal structure of reduced 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 / metal ion binding
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp 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 / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp 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 / SYNCHROTRON / rigid body refinement / Resolution: 1.45 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 1.3Oct 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 1.4Aug 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
Water6,287349
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
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
MethodPISA
4
A: Putidaredoxin
B: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1774
Polymers22,8262
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-46 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.070, 66.070, 154.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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 / 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.: 349 / 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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 18, 2002 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.45→27.92 Å / Num. all: 61499 / Num. obs: 60208 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 28.8
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5335 / Rsym value: 0.545 / % possible all: 92.7

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Processing

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

1oqr


Resolution: 1.45→27.92 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3036 5 %random
Rwork0.195 ---
all0.195 61374 --
obs0.195 60208 98.1 %-
Solvent computationSolvent model: Flat Model / Bsol: 42.6 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.45→27.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 12 349 2742
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 1.45→1.46 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.343 50 4.7 %
Rwork0.303 5335 -
obs-970 92.7 %

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