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- PDB-1oqr: Crystal structure of C73S mutant of putidaredoxin, a [2Fe-2S] fer... -

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Basic information

Entry
Database: PDB / ID: 1oqr
TitleCrystal structure of C73S mutant of putidaredoxin, a [2Fe-2S] ferredoxin from Pseudomonas putida, at 1.65A resolution
ComponentsPutidaredoxin
KeywordsELECTRON TRANSPORT / electron transfer
Function / homology
Function and homology information


P450-containing electron transport chain / 2 iron, 2 sulfur cluster binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSevrioukova, I.F. / Garcia, C. / Li, H. / Bhaskar, B. / Poulos, T.L.
CitationJournal: J.MOL.BIOL. / Year: 2003
Title: Crystal structure of putidaredoxin, the [2Fe-2S] component of the P450cam monooxygenase system from Pseudomonas putida
Authors: Sevrioukova, I.F. / Garcia, C. / Li, H. / Bhaskar, B. / Poulos, T.L.
History
DepositionMar 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_seq_id / _struct_conn.ptnr1_label_seq_id / _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 16, 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

Downloads & links

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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
Water4,035224
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 area1880 Å2
ΔGint-45 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.219, 66.219, 152.131
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
#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.: 224 / 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: 2.28 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: lithium sulfate, sodium citrate, dithiothreitol, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
2100 mMBis-Tris propane/acetate1droppH7.4
31.5 Mlithium sulfate1reservoir
450 mMsodium citrate1reservoirpH5.7

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Data collection

DiffractionMean temperature: 110 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: 1.65→50 Å / Num. all: 181573 / Num. obs: 180222 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 6.5
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.88 / Num. unique all: 1996 / Rsym value: 0.618 / % possible all: 97.8
Reflection
*PLUS
Highest resolution: 1.67 Å / Num. obs: 39004 / % possible obs: 96.7 % / Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: putidaredoxin C73S/C85S mutant, PDB ID code 1OQQ

1oqq


Resolution: 1.65→27.65 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1996 5 %RANDOM
Rwork0.237 ---
obs0.237 39983 96 %-
all-41840 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.0092 Å2 / ksol: 0.400588 e/Å3
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.57 Å20 Å20 Å2
2---3.57 Å20 Å2
3---7.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.65→27.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 12 224 2617
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 1.65→1.71 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.321 174 4.4 %
Rwork0.292 3815 -
obs-3997 97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3FES_4.PAR
Refinement
*PLUS
Highest resolution: 1.67 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06

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