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- PDB-2i7s: Crystal structure of Re(phen)(CO)3 (Thr124His)(His83Gln) Azurin C... -

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Basic information

Entry
Database: PDB / ID: 2i7s
TitleCrystal structure of Re(phen)(CO)3 (Thr124His)(His83Gln) Azurin Cu(II) from Pseudomonas aeruginosa
ComponentsAzurin
KeywordsELECTRON TRANSPORT / Azurin / Rhenium / Electron Transfer in proteins
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
COBALT TETRAAMMINE ION / COPPER (II) ION / Chem-REP / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsGradinaru, C. / Crane, B.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Relaxation dynamics of Pseudomonas aeruginosa Re(I)(CO)3(alpha-diimine)(HisX)+ (X = 83, 107, 109, 124, 126)Cu(II) azurins.
Authors: Blanco-Rodriguez, A.M. / Busby, M. / Ronayne, K. / Towrie, M. / Gradinaru, C. / Sudhamsu, J. / Sykora, J. / Hof, M. / Zalis, S. / Di Bilio, A.J. / Crane, B.R. / Gray, H.B. / Vlcek, A.
History
DepositionAug 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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.ptnr2_auth_asym_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_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.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 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
C: Azurin
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,13413
Polymers55,9514
Non-polymers2,1839
Water8,359464
1
A: Azurin
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0046
Polymers27,9762
Non-polymers1,0284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-15 kcal/mol
Surface area12800 Å2
MethodPISA
2
B: Azurin
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1317
Polymers27,9762
Non-polymers1,1555
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-16 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.135, 58.980, 66.107
Angle α, β, γ (deg.)82.920, 78.110, 76.680
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Azurin


Mass: 13987.839 Da / Num. of mol.: 4 / Mutation: H83Q, T124H
Source method: isolated from a genetically manipulated source
Details: Rhenium-modified azurin / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu / 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.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-REP / (1,10 PHENANTHROLINE)-(TRI-CARBON MONOXIDE) RHENIUM (I)


Mass: 450.443 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H8N2O3Re
#4: Chemical ChemComp-CON / COBALT TETRAAMMINE ION


Mass: 127.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH12N4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG4000, 100 mM LiNO3, 100 mM Imidazole pH 7.0. One fourth of the drop volume was saturated with [Co(NH3)5Cl]Cl2 solution, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.916 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 171226 / Num. obs: 104393 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 1.64 % / Rsym value: 0.08 / Net I/σ(I): 4.7

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BEX

1bex


Resolution: 1.35→30 Å / Isotropic thermal model: anisotropic / Cross valid method: FREE-R / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: LEAST-SQUARES ANISOTROPIC REFINEMENT USING THE KONNERT-HENDRICKSON CONJUGATE-GRADIENT ALGORITHM
RfactorNum. reflection% reflectionSelection details
Rfree0.239 150 -RANDOM
Rwork0.205 ---
all0.205 104393 --
obs-99883 95.6 %-
Displacement parametersBiso mean: 26.211 Å2
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 93 464 4491

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