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- PDB-2oj1: Disulfide-linked dimer of azurin N42C/M64E double mutant -

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Basic information

Entry
Database: PDB / ID: 2oj1
TitleDisulfide-linked dimer of azurin N42C/M64E double mutant
ComponentsAzurin
KeywordsELECTRON TRANSPORT / cupredoxin / electron transfer / engineered dimer
Function / homology
Function and homology information


transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding
Similarity search - Function
Azurin / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Authorsde Jongh, T.E. / Hoffmann, M. / Einsle, O. / Cavazzini, D. / Rossi, G.L. / Ubbink, M. / Canters, G.W.
CitationJournal: Eur.J.Inorg.Chem. / Year: 2007
Title: Inter- and intramolecular electron transfer in modified azurin dimers
Authors: de Jongh, T.E. / Hoffmann, M. / Einsle, O. / Cavazzini, D. / Rossi, G.L. / Ubbink, M. / Canters, G.W.
History
DepositionJan 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Azurin
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0254
Polymers27,8982
Non-polymers1272
Water2,738152
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0122
Polymers13,9491
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0122
Polymers13,9491
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.570, 116.980, 30.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Azurin


Mass: 13948.757 Da / Num. of mol.: 2 / Mutation: N42C, M64E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu / Plasmid: pTJ01 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00282
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.1
Details: 30 % PEG 4000, 0.1M sodium citrate buffer, pH 3.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 24, 2004 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→34.3 Å / Num. all: 10903 / Num. obs: 10369 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 3.88 % / Biso Wilson estimate: 47.5 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.91 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1405 / % possible all: 95.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOLREPphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P. aeruginosa azurin wildtype

Resolution: 2.3→34.3 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 725 -random
Rwork0.208 ---
all-10903 --
obs-10369 95.1 %-
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.959 Å20 Å20 Å2
2--10.566 Å20 Å2
3----11.526 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 2 152 2100
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.034
X-RAY DIFFRACTIONc_angle_deg2.843

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