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- PDB-7u2f: G116F Pseudomonas aeruginosa azurin -

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Basic information

Entry
Database: PDB / ID: 7u2f
TitleG116F Pseudomonas aeruginosa azurin
ComponentsAzurin
KeywordsELECTRON TRANSPORT / G116F mutant / Pseudomonas aeruginosa / azurin / redox potential tuning / phenylalanine / secondary coordination sphere
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: 2.2 Å
AuthorsLiu, Y. / Lu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2201279 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
DepositionFeb 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 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)14,3014
Polymers14,0521
Non-polymers2493
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-3 kcal/mol
Surface area6640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.172, 49.172, 261.961
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Azurin


Mass: 14051.921 Da / Num. of mol.: 1 / Fragment: UNP residues 21-148 / Mutation: G116F
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 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3 uL 1.4 mM in 100 mM sodium acetate, pH 5.6 + 1 uL reservoir buffer (20% PEG4000, 100 mM Tris-HCl, pH 8.0, 10 mM copper(II) sulfate, 100 mM lithium nitrate) against 250 uL reservoir buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 18, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.2→42.58 Å / Num. obs: 10424 / % possible obs: 99.6 % / Redundancy: 18 % / Biso Wilson estimate: 66.08 Å2 / CC1/2: 0.998 / Net I/σ(I): 20.78
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 1006 / CC1/2: 0.708 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4AZU

4azu


Resolution: 2.2→42.58 Å / SU ML: 0.3998 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.7106
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2557 1040 10 %
Rwork0.221 9364 -
obs0.2247 10404 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.93 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 10 28 1018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00281005
X-RAY DIFFRACTIONf_angle_d0.54621355
X-RAY DIFFRACTIONf_chiral_restr0.0425152
X-RAY DIFFRACTIONf_plane_restr0.0039174
X-RAY DIFFRACTIONf_dihedral_angle_d5.2945134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.40381420.36861292X-RAY DIFFRACTION100
2.32-2.460.37211470.32381314X-RAY DIFFRACTION100
2.46-2.650.36621410.3251272X-RAY DIFFRACTION99.72
2.65-2.920.33071470.31551319X-RAY DIFFRACTION100
2.92-3.340.34631480.26691330X-RAY DIFFRACTION100
3.34-4.210.22861510.20991366X-RAY DIFFRACTION99.67
4.21-42.580.20421640.16711471X-RAY DIFFRACTION98.14
Refinement TLS params.Method: refined / Origin x: 4.89749069655 Å / Origin y: -16.2824755597 Å / Origin z: 9.93376984892 Å
111213212223313233
T0.491969561306 Å20.0762219685658 Å2-0.00991828024833 Å2-0.571332754887 Å2-0.141337905673 Å2--0.479033637823 Å2
L5.57152755952 °20.341900840093 °21.05400494906 °2-4.17378951612 °20.624972511188 °2--3.24743365342 °2
S-0.296996725911 Å °-0.610881929771 Å °0.55026039815 Å °0.443055834431 Å °0.0821981236328 Å °-0.0536113320801 Å °-0.163115340473 Å °-0.208832406288 Å °0.164059782746 Å °
Refinement TLS groupSelection details: all

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