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- PDB-2fnw: Pseudomonas aeruginosa E2Q/H83Q/M109H-azurin RE(PHEN)(CO)3 -

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Basic information

Entry
Database: PDB / ID: 2fnw
TitlePseudomonas aeruginosa E2Q/H83Q/M109H-azurin RE(PHEN)(CO)3
ComponentsAzurin
KeywordsMETAL BINDING PROTEIN / BLUE-COPPER / ELECTRON-TRANSFER / RHENIUM / INFRARED SPECTROSCOPY
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
COPPER (II) ION / Chem-REP / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGradinaru, C. / Crane, B.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Excited-state dynamics of structurally characterized [ReI(CO)3(phen)(HisX)]+ (X = 83, 109) Pseudomonas aeruginosa azurins in aqueous solution.
Authors: Busby, M. / Gradinaru, C. / Crane, B.R. / Di Bilio, A.J. / Matousek, P. / Towrie, M. / Leigh, B.S. / Richards, J.H. / Vlcek, A. / Gray, H.B.
History
DepositionJan 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 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_alt_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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.pdbx_aromatic_flag

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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)28,9436
Polymers27,9152
Non-polymers1,0284
Water3,873215
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4723
Polymers13,9581
Non-polymers5142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4723
Polymers13,9581
Non-polymers5142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.935, 38.334, 48.835
Angle α, β, γ (deg.)100.50, 106.25, 109.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Azurin


Mass: 13957.747 Da / Num. of mol.: 2 / Mutation: E2Q/H83Q/M109H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: AZU, PA4922 / Production host: Escherichia coli (E. coli) / References: UniProt: P00282
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C15H8N2O3Re
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 1.79 Å3/Da / Density % sol: 31.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG molecular weight 4000, 100 mM LiNO3 and 100 mM imidazole pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.945 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 4, 2002
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.945 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 46662 / Num. obs: 31077 / % possible obs: 66.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.086 / Net I/σ(I): 17.4
Reflection shellResolution: 1.3→1.35 Å / Mean I/σ(I) obs: 1.8 / Num. unique all: 156 / Rsym value: 0.352 / % possible all: 3.3

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1BEX

1bex


Resolution: 1.4→30 Å / Num. parameters: 9172 / Num. restraintsaints: 8468
Isotropic thermal model: Heavy atoms (Cu, Re, S) anisotropic
Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2476 5 %RANDOM
Rwork0.196 ---
all0.195 38090 --
obs-30514 80.11 %-
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2202
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 86 215 2262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0417
X-RAY DIFFRACTIONs_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.083
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.4→1.45 Å
RfactorNum. reflection% reflection
Rwork0.418 --
obs-859 22.77 %

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