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- PDB-7tnc: M13F/G116F Pseudomonas aeruginosa azurin -

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Basic information

Entry
Database: PDB / ID: 7tnc
TitleM13F/G116F Pseudomonas aeruginosa azurin
ComponentsAzurin
KeywordsELECTRON TRANSPORT / Electron transfer 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: 1.47 Å
AuthorsLiu, Y. / Lu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1726244 United States
CitationJournal: Inorg.Chem. / Year: 2023
Title: Structural Basis for the Effects of Phenylalanine on Tuning the Reduction Potential of Type 1 Copper in Azurin.
Authors: Liu, Y. / Marshall, N.M. / Yu, S.S. / Kim, W. / Gao, Y.G. / Robinson, H. / Nilges, M.J. / Zhang, Y. / New, S.Y. / Lu, Y.
History
DepositionJan 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 25, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3535
Polymers14,0681
Non-polymers2854
Water3,171176
1
A: Azurin
hetero molecules

A: Azurin
hetero molecules

A: Azurin
hetero molecules

A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,41020
Polymers56,2724
Non-polymers1,13916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area6190 Å2
ΔGint-50 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.274, 73.901, 77.616
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-204-

CL

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Components

#1: Protein Azurin


Mass: 14067.899 Da / Num. of mol.: 1 / Mutation: M13F, G116F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: azu, PA4922 / Production host: Escherichia coli (E. coli) / References: UniProt: P00282
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.02 % / Description: Diamond-shaped blue crystals.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: The 1.4 mM apo-protein was prepared in 100 mM pH=5.6 NaOAc buffer. For each well, add 300 uL reservoir buffer containing 100 mM pH=8.0 Tris-HCl, 10 mM CuSO4 and 20% PEG-4000. 3 uL of protein ...Details: The 1.4 mM apo-protein was prepared in 100 mM pH=5.6 NaOAc buffer. For each well, add 300 uL reservoir buffer containing 100 mM pH=8.0 Tris-HCl, 10 mM CuSO4 and 20% PEG-4000. 3 uL of protein stock was mixed with 1 uL reservoir buffer on the glass slides and sealed on the wells. Diamond-shaped blue crystals grew within 4 days.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→41 Å / Num. obs: 24023 / % possible obs: 99 % / Redundancy: 6 % / Biso Wilson estimate: 14.83 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.09367 / Rrim(I) all: 0.103 / Net I/σ(I): 8.87
Reflection shellResolution: 1.47→1.523 Å / Rmerge(I) obs: 0.3451 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2009 / CC1/2: 0.891 / CC star: 0.971 / Rrim(I) all: 0.3949

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4azu

4azu


Resolution: 1.47→41 Å / SU ML: 0.1959 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0246
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 2350 5.24 %
Rwork0.2044 42462 -
obs0.2061 24023 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.48 Å2
Refinement stepCycle: LAST / Resolution: 1.47→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 11 176 1171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581028
X-RAY DIFFRACTIONf_angle_d0.86461391
X-RAY DIFFRACTIONf_chiral_restr0.0812155
X-RAY DIFFRACTIONf_plane_restr0.0042181
X-RAY DIFFRACTIONf_dihedral_angle_d15.6121375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50.3073860.30011767X-RAY DIFFRACTION67.63
1.5-1.530.33091040.29252018X-RAY DIFFRACTION77.59
1.53-1.570.38171360.27822380X-RAY DIFFRACTION92.57
1.57-1.610.3051620.27732601X-RAY DIFFRACTION99.6
1.61-1.650.28091380.26422585X-RAY DIFFRACTION99.78
1.65-1.70.30831460.25732606X-RAY DIFFRACTION99.67
1.7-1.750.27621670.27072548X-RAY DIFFRACTION99.16
1.75-1.820.2396930.25282609X-RAY DIFFRACTION99.52
1.82-1.890.37061400.25142632X-RAY DIFFRACTION99.93
1.89-1.980.25861760.23352558X-RAY DIFFRACTION99.82
1.98-2.080.26031510.21932543X-RAY DIFFRACTION99.3
2.08-2.210.25831730.20942545X-RAY DIFFRACTION99.56
2.21-2.380.27721390.21282625X-RAY DIFFRACTION100
2.38-2.620.23221510.20552597X-RAY DIFFRACTION99.96
2.62-30.2131070.18142625X-RAY DIFFRACTION99.93
3-3.780.20211350.16792614X-RAY DIFFRACTION100
3.78-410.15721460.14972609X-RAY DIFFRACTION99.89

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