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- PDB-1jvo: Azurin dimer, crosslinked via disulfide bridge -

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Basic information

Entry
Database: PDB / ID: 1jvo
TitleAzurin dimer, crosslinked via disulfide bridge
ComponentsAzurin
KeywordsELECTRON TRANSPORT / cupredoxin / electron transfer / covalent crosslink
Function / homology
Function and homology information


transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding / plasma membrane
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
Authorsvan Amsterdam, I.M.C. / Ubbink, M. / Einsle, O. / Messerschmidt, A. / Merli, A. / Cavazzini, D. / Rossi, G.L. / Canters, G.W.
Citation
Journal: Nat.Struct.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.
#1: Journal: Chemistry / Year: 2001
Title: Effects of Dimerization on Protein Electron Transfer
Authors: van Amsterdam, I.M.C. / Ubbink, M. / Jeuken, L.J.C. / Verbeet, M.P. / Einsle, O. / Messerschmidt, A. / Canters, G.W.
History
DepositionAug 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Azurin
B: Azurin
C: Azurin
D: Azurin
E: Azurin
F: Azurin
G: Azurin
H: Azurin
I: Azurin
J: Azurin
K: Azurin
L: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,17324
Polymers167,41012
Non-polymers76312
Water00
1
A: Azurin
B: Azurin
C: Azurin
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0588
Polymers55,8034
Non-polymers2544
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Azurin
F: Azurin
G: Azurin
H: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0588
Polymers55,8034
Non-polymers2544
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Azurin
J: Azurin
K: Azurin
L: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0588
Polymers55,8034
Non-polymers2544
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.323, 94.425, 193.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsFOUR MONOMERS GENERATE A TETRAMER ACTIVE IN INTERMOLECULAR ELECTRON TRANSFER. THE ASYMMETRIC UNIT CONTAINS THREE SUCH TETRAMERS. PROGRAM PISA DOES NOT PREDICT THOSE ASSEMBLIES BECAUSE THE INDIVIDUAL INTERMOLECULAR DISULFIDE BOND DOES NOT CREATE SUFFICIENT BURIED AREA.

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Components

#1: Protein
Azurin


Mass: 13950.839 Da / Num. of mol.: 12 / Fragment: Azurin / Mutation: N42C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu / Plasmid: pGK22 / 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.: 12 / Source method: obtained synthetically / Formula: Cu
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 8000, Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 293K, temperature 293.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
220 %(w/v)PEG80001reservoir
30.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 9, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 41247 / Num. obs: 35555 / % possible obs: 86.2 % / Observed criterion σ(I): 3 / Redundancy: 1.9 % / Biso Wilson estimate: 60.1 Å2 / Rsym value: 0.101 / Net I/σ(I): 7.1
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 3588 / Rsym value: 0.404 / % possible all: 88.2
Reflection
*PLUS
Num. obs: 42605 / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
% possible obs: 86.4 % / Rmerge(I) obs: 0.484

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: CHAINS F AND K ARE PARTIALLY DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1072 3 %RANDOM
Rwork0.244 ---
all-41909 --
obs-35555 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.483 Å20 Å20 Å2
2--7.805 Å20 Å2
3----11.289 Å2
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11664 0 12 0 11676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0093
X-RAY DIFFRACTIONc_angle_deg1.38
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.239 / Rfactor Rfree: 0.293
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.34

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