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- PDB-8f5k: Azurin from Pseudomonas aeruginosa, Y72F/Y108F/F110A mutant -

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Basic information

Entry
Database: PDB / ID: 8f5k
TitleAzurin from Pseudomonas aeruginosa, Y72F/Y108F/F110A mutant
ComponentsAzurin
KeywordsELECTRON TRANSPORT / copper protein
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. / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsZeug, M. / Offenbacher, A.R. / Choe, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)20-03956 United States
CitationJournal: J.Phys.Chem.B / Year: 2023
Title: Electrochemical and Structural Study of the Buried Tryptophan in Azurin: Effects of Hydration and Polarity on the Redox Potential of W48.
Authors: Tyson, K. / Tangtartharakul, C.B. / Zeug, M. / Findling, N. / Haddy, A. / Hvastkovs, E. / Choe, J.Y. / Kim, J.E. / Offenbacher, A.R.
History
DepositionNov 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)63,8798
Polymers63,6254
Non-polymers2544
Water14,682815
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9702
Polymers15,9061
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9702
Polymers15,9061
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9702
Polymers15,9061
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9702
Polymers15,9061
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.425, 64.818, 71.149
Angle α, β, γ (deg.)90.00, 90.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Azurin


Mass: 15906.318 Da / Num. of mol.: 4 / Mutation: Y72F,Y108F,F110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu / Production host: Escherichia coli (E. coli) / References: UniProt: P00282
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 815 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 31.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22-25 % (w/v) PEG 3350, 0.1 M Hepes, pH 7.0, 0.2 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 117338 / % possible obs: 95.7 % / Redundancy: 3.1 % / CC1/2: 0.996 / Rsym value: 0.059 / Net I/σ(I): 22.9
Reflection shellResolution: 1.25→1.27 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5678 / CC1/2: 0.69 / Rsym value: 0.598

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3fqy

3fqy


Resolution: 1.25→40.28 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1794 5879 5.01 %
Rwork0.1578 --
obs0.1589 117303 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→40.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3818 0 4 815 4637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083905
X-RAY DIFFRACTIONf_angle_d0.9675263
X-RAY DIFFRACTIONf_dihedral_angle_d6.424509
X-RAY DIFFRACTIONf_chiral_restr0.073601
X-RAY DIFFRACTIONf_plane_restr0.007685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.30982010.28573277X-RAY DIFFRACTION85
1.27-1.280.30552200.2623612X-RAY DIFFRACTION94
1.28-1.30.24491800.25123679X-RAY DIFFRACTION94
1.3-1.310.21621720.23543656X-RAY DIFFRACTION95
1.31-1.330.26441880.21683656X-RAY DIFFRACTION94
1.33-1.350.22622130.22253641X-RAY DIFFRACTION95
1.35-1.370.24311770.21073697X-RAY DIFFRACTION95
1.37-1.390.2411880.20873681X-RAY DIFFRACTION95
1.39-1.410.23381990.20533743X-RAY DIFFRACTION95
1.41-1.430.21062250.19693648X-RAY DIFFRACTION96
1.43-1.460.23271970.19483758X-RAY DIFFRACTION96
1.46-1.490.22461940.18373676X-RAY DIFFRACTION96
1.49-1.510.20951920.17693728X-RAY DIFFRACTION96
1.51-1.550.21861650.17493781X-RAY DIFFRACTION96
1.55-1.580.19292140.17083732X-RAY DIFFRACTION96
1.58-1.620.20092020.1633728X-RAY DIFFRACTION97
1.62-1.660.17282180.16223751X-RAY DIFFRACTION97
1.66-1.70.1731860.16093779X-RAY DIFFRACTION97
1.7-1.750.18781820.15943772X-RAY DIFFRACTION97
1.75-1.810.17311630.15823808X-RAY DIFFRACTION97
1.81-1.870.16781960.15853799X-RAY DIFFRACTION97
1.87-1.950.17021820.15673805X-RAY DIFFRACTION97
1.95-2.040.17182400.14683750X-RAY DIFFRACTION97
2.04-2.140.16831960.14583830X-RAY DIFFRACTION98
2.14-2.280.16452070.14333770X-RAY DIFFRACTION97
2.28-2.450.17561970.14683812X-RAY DIFFRACTION97
2.45-2.70.16471850.14253784X-RAY DIFFRACTION97
2.7-3.090.16322230.14133737X-RAY DIFFRACTION95
3.09-3.890.15752070.12683737X-RAY DIFFRACTION95
3.89-40.280.14811700.14293597X-RAY DIFFRACTION89
Refinement TLS params.Method: refined / Origin x: 11.2234 Å / Origin y: -24.1644 Å / Origin z: 18.6797 Å
111213212223313233
T0.065 Å2-0.002 Å2-0.0021 Å2-0.0816 Å20.0056 Å2--0.0723 Å2
L0.5219 °20.0515 °20.0097 °2-0.3639 °2-0.0288 °2--0.3522 °2
S0.0067 Å °0.0213 Å °-0.0118 Å °-0.0066 Å °0.0052 Å °-0.0292 Å °0.0188 Å °-0.0188 Å °-0.0112 Å °
Refinement TLS groupSelection details: all

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