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- PDB-7tc5: All Phe-Azurin variant - F15Y -

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Basic information

Entry
Database: PDB / ID: 7tc5
TitleAll Phe-Azurin variant - F15Y
ComponentsAzurin
KeywordsELECTRON TRANSPORT / copper ion binding / cupredoxin / azurin / metal ion binding
Function / homology
Function and homology information


periplasmic space / electron transfer activity / oxidoreductase activity / copper ion 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 / NITRATE ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsFedoretz-Maxwell, B.P. / Worrall, L.J. / Strynadka, N.C.J. / Warren, J.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN 06272 Canada
CitationJournal: Inorg.Chem. / Year: 2022
Title: The Impact of Second Coordination Sphere Methionine-Aromatic Interactions in Copper Proteins.
Authors: Fedoretz-Maxwell, B.P. / Shin, C.H. / MacNeil, G.A. / Worrall, L.J. / Park, R. / Strynadka, N.C.J. / Walsby, C.J. / Warren, J.J.
History
DepositionDec 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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

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Assembly

Deposited unit
A: Azurin
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1437
Polymers27,8682
Non-polymers2765
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.451, 53.830, 133.791
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Azurin


Mass: 13933.787 Da / Num. of mol.: 2 / Mutation: F15Y, W48F, Y72F, H83Q, Y108F, T124H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A514YDB7
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mg/mL protein in 0.1 M NaOAc (pH 5.0), 26.5-29% PEG 4000, 100 mM lithium nitrate, 10 mM copper sulfate, and 100 mM tris (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.4→44.6 Å / Num. obs: 45146 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.5
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2184 / CC1/2: 0.683 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
MOLREP11phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AZU

4azu


Resolution: 1.45→41.97 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.596 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2528 5.1 %RANDOM
Rwork0.1829 ---
obs0.1845 45146 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.13 Å2 / Biso mean: 23.548 Å2 / Biso min: 12.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.45→41.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 8 212 2164
Biso mean--23.47 33.07 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132017
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161888
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.6352722
X-RAY DIFFRACTIONr_angle_other_deg1.5491.5934380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2565262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51226.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80415363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.899152
X-RAY DIFFRACTIONr_chiral_restr0.090.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022348
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02428
LS refinement shellResolution: 1.45→1.47 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.365 196 -
Rwork0.363 3471 -
obs--99.65 %

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