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- PDB-2idf: P. aeruginosa azurin N42C/M64E double mutant, BMME-linked dimer -

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Basic information

Entry
Database: PDB / ID: 2idf
TitleP. aeruginosa azurin N42C/M64E double mutant, BMME-linked dimer
ComponentsAzurin
KeywordsELECTRON TRANSPORT / protein crosslinking / cupredoxins / electron transfer
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
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / COPPER (II) ION / NICKEL (II) ION / Chem-OPP / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsEinsle, O. / de Jongh, T.E. / Hoffmann, M. / Cavazzini, D. / Rossi, G.L. / Ubbink, M. / Canters, G.W.
Citation
Journal: To be Published
Title: Electron transfer in a crosslinked protein dimer mediated by a hydrogen-bonded network across the dimer interface
Authors: de Jongh, T.E. / Hoffmann, M. / Einsle, O. / Cavazzini, D. / Rossi, G.L. / Ubbink, M. / Canters, G.W.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2002
Title: Dramatic modulation of electron transfer in protein complexes by crosslinking
Authors: van Amsterdam, I.M.C. / Ubbink, M. / Einsle, O. / Messerschmidt, A. / Merli, A. / Cavazzini, D. / Rossi, G.L. / Canters, G.W.
History
DepositionSep 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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 1.3Aug 30, 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: Azurin
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6229
Polymers27,8982
Non-polymers7257
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-24.3 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.004, 48.004, 283.399
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#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: pET (Novagen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00282

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Non-polymers , 5 types, 128 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3
#5: Chemical ChemComp-OPP / 1-[PYRROL-1-YL-2,5-DIONE-METHOXYMETHYL]-PYRROLE-2,5-DIONE


Mass: 236.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N2O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.38 Å3/Da / Density % sol: 63.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 25% PEG 2000 MME, 10 mM NiCl2, 100 mM Tris/HCl, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 14, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 17287 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.81 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.0629 / Net I/σ(I): 12.28
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.3172 / Mean I/σ(I) obs: 3.44 / Num. unique all: 2109 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1JVO

1jvo


Resolution: 2.25→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 843 -RANDOM
Rwork0.2191 ---
all-16882 --
obs-16039 96.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.501 Å2-3.817 Å2-3.501 Å2
2--0 Å27.003 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 37 121 2104
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0061
X-RAY DIFFRACTIONc_angle_deg1.2664

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