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- PDB-1jvl: Azurin dimer, covalently crosslinked through bis-maleimidomethylether -

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Basic information

Entry
Database: PDB / ID: 1jvl
TitleAzurin dimer, covalently crosslinked through bis-maleimidomethylether
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
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / COPPER (II) ION / NICKEL (II) ION / Chem-OPP / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6279
Polymers27,9022
Non-polymers7257
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-28 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.605, 48.605, 284.809
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61
DetailsThe true spacegroup of the data is P6122, but the structure was refined in P61 to be able to build a dimer, which is linked via BMME across a crystallographic twofold. Strict NCS restraints were applied.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Azurin


Mass: 13950.839 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 121 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.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 2000 MME, nickel chloride, Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 293K
Crystal grow
*PLUS
pH: 9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
220 %(w/v)PEG2000 MME1reservoir
30.01 M1reservoirNiCl2
40.1 MTris-HCl1reservoirpH9.0

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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→50 Å / Num. all: 25663 / Num. obs: 25535 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Biso Wilson estimate: 39.73 Å2 / Rsym value: 0.072 / Net I/σ(I): 15
Reflection shellResolution: 2→2.06 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2093 / Rsym value: 0.44 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.44

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1227 4.8 %RANDOM
Rwork0.19 ---
all-25663 --
obs-25535 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.659 Å21.185 Å20 Å2
2---2.659 Å20 Å2
3---5.317 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 37 114 2095
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0054

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