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- PDB-9oh6: H117A/M121H Azurin with Cu(II), pH 7.7 -

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Basic information

Entry
Database: PDB / ID: 9oh6
TitleH117A/M121H Azurin with Cu(II), pH 7.7
ComponentsAzurin
KeywordsOXIDOREDUCTASE / Metal binding mutant azurin 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 / 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. / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsVan Stappen, C. / Lu, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2420683 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM145134 United States
Robert A. Welch FoundationF-0020 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Beyond Blue: Systematic Modulation of Electronic Structure and Redox Properties of Type 1 Copper in Azurin.
Authors: Van Stappen, C. / Xu, J. / Liu, Y. / Van Stappen, J. / Kim, W. / Zhang, Y.J. / Lu, Y.
History
DepositionMay 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Azurin
E: Azurin
H: Azurin
K: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,60416
Polymers55,6074
Non-polymers99712
Water9,980554
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.905, 48.836, 81.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Azurin


Mass: 13901.681 Da / Num. of mol.: 4 / Mutation: H117A, M121H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: azu, PA4922 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00282
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: Well buffer: 27% PEG 4000, 100 mM LiNO3, 50 mM Tris at pH 7.7 Protein stock: 1.5 mM in 25 mM Tris pH 7.8, 1.8 mM CuSO4 Crystallization drop: 1 uL protein stock + 3 uL well buffer
Temp details: Cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 4, 2024
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.04→81.31 Å / Num. obs: 29554 / % possible obs: 99.26 % / Redundancy: 3.36 % / Biso Wilson estimate: 19.57 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.094 / Rrim(I) all: 0.175 / Net I/σ(I): 6.3
Reflection shellResolution: 2.04→2.07 Å / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1389 / CC1/2: 0.269 / Rpim(I) all: 0.365 / Rrim(I) all: 0.662 / % possible all: 96.26

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALS2data reduction
DIALS2data scaling
PHENIX1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→81.31 Å / SU ML: 0.2041 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2328 1474 5 %
Rwork0.1764 28014 -
obs0.1791 29488 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.72 Å2
Refinement stepCycle: LAST / Resolution: 2.04→81.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 0 40 554 4478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663980
X-RAY DIFFRACTIONf_angle_d0.83975372
X-RAY DIFFRACTIONf_chiral_restr0.0501604
X-RAY DIFFRACTIONf_plane_restr0.0057696
X-RAY DIFFRACTIONf_dihedral_angle_d7.6723540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.10.27921300.22022456X-RAY DIFFRACTION96.93
2.1-2.180.25311510.2012492X-RAY DIFFRACTION99.03
2.18-2.270.25681490.20162525X-RAY DIFFRACTION99.11
2.27-2.370.27261450.1942506X-RAY DIFFRACTION99.25
2.37-2.50.24461400.192513X-RAY DIFFRACTION98.81
2.5-2.650.23721400.17512583X-RAY DIFFRACTION99.49
2.65-2.860.26811360.17872538X-RAY DIFFRACTION99.89
2.86-3.140.24881310.172557X-RAY DIFFRACTION99.45
3.14-3.60.20781190.15492582X-RAY DIFFRACTION99.19
3.6-4.530.17791160.15042624X-RAY DIFFRACTION99.67
4.54-81.310.22041170.18452638X-RAY DIFFRACTION98.64

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