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- PDB-7tc6: All Phe-Azurin variant - F15W -

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Basic information

Entry
Database: PDB / ID: 7tc6
TitleAll Phe-Azurin variant - F15W
ComponentsAzurin
KeywordsELECTRON TRANSPORT / copper ion binding / cupredoxin / azurin / metal ion binding
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 / NITRATE ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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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)28,1666
Polymers27,9142
Non-polymers2534
Water3,297183
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)54.782, 59.525, 74.342
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: 13956.823 Da / Num. of mol.: 2 / Mutation: F15W, W48F, Y72F, H83Q, Y108F, T124H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu, PA4922 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00282
#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-NO3 / NITRATE ION


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


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.17 Å3/Da / Density % sol: 43.35 %
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: APS / Beamline: 23-ID-B / Wavelength: 1.03324 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
ReflectionResolution: 1.85→44.14 Å / Num. obs: 20615 / % possible obs: 96.7 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.054 / Net I/σ(I): 11.4
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 999 / CC1/2: 0.89 / % possible all: 76.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
MOLREP11phasing
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AZU

4azu


Resolution: 1.85→44.14 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.693 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.153
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 1038 5.035 %RANDOM
Rwork0.1891 19577 --
all0.192 ---
obs-20615 96.377 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.607 Å2
Baniso -1Baniso -2Baniso -3
1--0.011 Å20 Å2-0 Å2
2---0.075 Å20 Å2
3---0.086 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 7 183 2138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131990
X-RAY DIFFRACTIONr_bond_other_d0.0060.0161863
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.6332677
X-RAY DIFFRACTIONr_angle_other_deg1.3931.5934317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6345254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78826.13688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16315356
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg18.518151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.434152
X-RAY DIFFRACTIONr_chiral_restr0.0660.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022284
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02422
X-RAY DIFFRACTIONr_nbd_refined0.2290.2409
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21757
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2976
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21015
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2133
X-RAY DIFFRACTIONr_metal_ion_refined0.5470.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2060.212
X-RAY DIFFRACTIONr_nbd_other0.2150.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.216
X-RAY DIFFRACTIONr_mcbond_it2.2562.5611022
X-RAY DIFFRACTIONr_mcbond_other2.2412.5571021
X-RAY DIFFRACTIONr_mcangle_it3.393.8251274
X-RAY DIFFRACTIONr_mcangle_other3.3933.8291275
X-RAY DIFFRACTIONr_scbond_it2.8912.892968
X-RAY DIFFRACTIONr_scbond_other2.8912.894968
X-RAY DIFFRACTIONr_scangle_it4.514.1861403
X-RAY DIFFRACTIONr_scangle_other4.5054.1871403
X-RAY DIFFRACTIONr_lrange_it5.86531.2682210
X-RAY DIFFRACTIONr_lrange_other5.85831.2462207
LS refinement shellResolution: 1.85→1.898 Å
RfactorNum. reflection% reflection
Rfree0.275 57 -
Rwork0.268 1156 -
obs--77.2611 %

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