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- PDB-1jzf: Pseudomonas aeruginosa Oxidized Azurin(Cu2+) Ru(tpy)(phen)(His83) -

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Basic information

Entry
Database: PDB / ID: 1jzf
TitlePseudomonas aeruginosa Oxidized Azurin(Cu2+) Ru(tpy)(phen)(His83)
ComponentsAZURIN
KeywordsELECTRON TRANSPORT / Blue-copper / Electron Transfer / Tunneling / Ruthenium / Cu2+
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 / TETRA(IMIDAZOLE)DIAQUACOPPER (II) / Chem-RTB / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsCrane, B.R. / Di Bilio, A.J. / Winkler, J.R. / Gray, H.B.
CitationJournal: J.Am.Chem.Soc. / Year: 2001
Title: Electron tunneling in single crystals of Pseudomonas aeruginosa azurins.
Authors: Crane, B.R. / Di Bilio, A.J. / Winkler, J.R. / Gray, H.B.
History
DepositionSep 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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.ptnr1_label_seq_id / _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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9084
Polymers13,9621
Non-polymers9463
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.776, 61.441, 75.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-902-

IME

21A-902-

IME

31A-1058-

HOH

41A-1108-

HOH

51A-1111-

HOH

61A-1118-

HOH

71A-1174-

HOH

DetailsThe biological assembly is a monomer

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Components

#1: Protein AZURIN


Mass: 13961.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00282
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-RTB / (2,2':6',2'-TERPYRIDINE)-(1,10-PHENANTHROLINE) RUTHENIUM (II)


Mass: 514.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H19N5Ru
#4: Chemical ChemComp-IME / TETRA(IMIDAZOLE)DIAQUACOPPER (II)


Mass: 367.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16CuN8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 8 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120-30 mg/mlprotein1drop
240 mMimidazole1drop
32 mM1droppH7.2NaCl
4100 mMimidazole1reservoirpH6.0-8.0
5100 mM1reservoirLiNO3
66.25 mM1reservoirCuCl2
725-38 %PEG4000-80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 5, 2000
RadiationMonochromator: Double Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 19968 / Num. obs: 19968 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.038 / Net I/σ(I): 32
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 0.118 / Num. unique all: 1919 / Rsym value: 0.153 / % possible all: 98.9
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 98.9 % / Rmerge(I) obs: 0.038

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNS1refinement
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→19.78 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 641862.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1539 7.8 %RANDOM
Rwork0.218 ---
all-19638 --
obs-19638 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.9323 Å2 / ksol: 0.352409 e/Å3
Displacement parametersBiso mean: 15.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å20 Å20 Å2
2--0.2 Å20 Å2
3---1.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 46 174 1235
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_mcbond_it0.31.5
X-RAY DIFFRACTIONc_mcangle_it0.552
X-RAY DIFFRACTIONc_scbond_it0.352
X-RAY DIFFRACTIONc_scangle_it0.562.5
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.259 157 8.5 %
Rwork0.249 1680 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19X.HEMEWATER.TOP
X-RAY DIFFRACTION3RUPHEN.PARRUPHEN.TOP
X-RAY DIFFRACTION4WATER.PARAMTOPH19X.HEME
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 7.8 % / Rfactor obs: 0.217 / Rfactor Rfree: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03
X-RAY DIFFRACTIONc_mcbond_it0.31.5
X-RAY DIFFRACTIONc_scbond_it0.352
X-RAY DIFFRACTIONc_mcangle_it0.552
X-RAY DIFFRACTIONc_scangle_it0.562.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.259 / % reflection Rfree: 8.5 % / Rfactor Rwork: 0.249

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