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- PDB-1r1c: PSEUDOMONAS AERUGINOSA W48F/Y72F/H83Q/Y108W-AZURIN RE(PHEN)(CO)3(... -

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Basic information

Entry
Database: PDB / ID: 1r1c
TitlePSEUDOMONAS AERUGINOSA W48F/Y72F/H83Q/Y108W-AZURIN RE(PHEN)(CO)3(HIS107)
ComponentsAzurin
KeywordsELECTRON TRANSPORT / BLUE-COPPER / ELECTRON-TRANSFER / RHENIUM / TUNNELING / RADICAL / EPR
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 (I) ION / Chem-REP / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMiller, J.E. / Gradinaru, C. / Crane, B.R. / Di Bilio, A.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Spectroscopy and reactivity of a photogenerated tryptophan radical in a structurally defined protein environment
Authors: Miller, J.E. / Gradinaru, C. / Crane, B.R. / Di Bilio, A.J. / Wehbi, W.A. / Un, S. / Winkler, J.R. / Gray, H.B.
History
DepositionSep 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
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
C: Azurin
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,77512
Polymers55,7194
Non-polymers2,0568
Water5,459303
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4443
Polymers13,9301
Non-polymers5142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4443
Polymers13,9301
Non-polymers5142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4443
Polymers13,9301
Non-polymers5142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4443
Polymers13,9301
Non-polymers5142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.947, 56.933, 77.296
Angle α, β, γ (deg.)90.00, 98.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Azurin


Mass: 13929.798 Da / Num. of mol.: 4 / Mutation: W48F/Y72F/H83Q/Q107H/Y108W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: AZU OR PA4922 / Plasmid: PET9A(ASA) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00282
#2: Chemical
ChemComp-CU1 / COPPER (I) 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 1.95 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000, lithium nitrate, imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
225 mMHEPES1droppH7.5
320 %PEG40001reservoir
4100 mM1reservoirLiNO3
5100 mMimidazole1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.964 / Wavelength: 0.964 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 8, 2002
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9641
20.9641
ReflectionResolution: 1.9→40 Å / Num. obs: 76883 / % possible obs: 98.8 % / Redundancy: 3.6 % / Rsym value: 0.075 / Net I/σ(I): 14
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.61 % / Mean I/σ(I) obs: 3.35 / Rsym value: 0.374 / % possible all: 97.8
Reflection
*PLUS
Highest resolution: 1.9 Å / Rmerge(I) obs: 0.075

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BEX

1bex


Resolution: 1.9→40 Å / Num. parameters: 17719 / Num. restraintsaints: 16833 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST. 28(1995)53-56.
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 3807 -RANDOM
Rwork0.2236 ---
all0.2236 76883 --
obs0.2236 73076 100 %-
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4279
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 151 303 4366
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0398
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.158
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.002
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.105
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.9→2 Å /
RfactorNum. reflection
Rwork0.388 -
obs-5518
Refinement
*PLUS
Highest resolution: 1.9 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS

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