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- PDB-9oh7: M13F/H117A/M121H Azurin with Cu(II), pH 7.4 -

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Basic information

Entry
Database: PDB / ID: 9oh7
TitleM13F/H117A/M121H Azurin with Cu(II), pH 7.4
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 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
A: Azurin
E: Azurin
G: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,66816
Polymers55,6714
Non-polymers99712
Water6,377354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.819, 48.492, 87.983
Angle α, β, γ (deg.)90.000, 93.420, 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: 13917.659 Da / Num. of mol.: 4 / Mutation: M13F, 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.: 354 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Well buffer: 30% PEG 4000, 100 mM LiNO3, 50 mM Tris at pH 7.4 Protein stock: 1.5 mM in 25 mM Tris pH 7.8, 1.8 mM CuSO4 Crystallization drop: 1.5 uL protein stock + 1.5 uL well buffer

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid N2 cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9747 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 29, 2024
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9747 Å / Relative weight: 1
ReflectionResolution: 2→87.83 Å / Num. obs: 32803 / % possible obs: 98.72 % / Redundancy: 3.417 % / Biso Wilson estimate: 26.37 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.076 / Rrim(I) all: 0.143 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3258 / CC1/2: 0.751 / Rpim(I) all: 0.362 / Rrim(I) all: 0.681 / % possible all: 99.12

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→87.83 Å / SU ML: 0.2996 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.1272
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 1660 5.06 %5%
Rwork0.212 31143 --
obs0.2146 32803 98.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.47 Å2
Refinement stepCycle: LAST / Resolution: 2→87.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 40 354 4290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00754006
X-RAY DIFFRACTIONf_angle_d0.92915411
X-RAY DIFFRACTIONf_chiral_restr0.0536605
X-RAY DIFFRACTIONf_plane_restr0.006703
X-RAY DIFFRACTIONf_dihedral_angle_d8.0051542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.35771210.28122584X-RAY DIFFRACTION99.05
2.06-2.130.36481170.27282600X-RAY DIFFRACTION98.91
2.13-2.20.33261480.26432531X-RAY DIFFRACTION96.82
2.2-2.290.32371190.26242557X-RAY DIFFRACTION97.7
2.29-2.390.3271360.25362589X-RAY DIFFRACTION99.78
2.39-2.520.31831600.2442625X-RAY DIFFRACTION99.71
2.52-2.680.32191730.2372542X-RAY DIFFRACTION99.52
2.68-2.880.30281560.23672601X-RAY DIFFRACTION99.46
2.88-3.170.27661410.22372535X-RAY DIFFRACTION97.38
3.18-3.630.22821340.1952630X-RAY DIFFRACTION98.57
3.63-4.580.21491350.17042624X-RAY DIFFRACTION99.5
4.58-87.830.18561200.17122725X-RAY DIFFRACTION98.37

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