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- PDB-8k9n: Subatomic resolution structure of Pseudoazurin from Alcaligenes f... -

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Basic information

Entry
Database: PDB / ID: 8k9n
TitleSubatomic resolution structure of Pseudoazurin from Alcaligenes faecalis
ComponentsPseudoazurin
KeywordsELECTRON TRANSPORT / copper-containing
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / 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 / Pseudoazurin
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.86 Å
AuthorsFukuda, Y. / Lintuluoto, M. / Kurihara, K. / Hasegawa, K. / Inoue, T. / Tamada, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Biochemistry / Year: 2024
Title: Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub- angstrom ngstrom Resolution X-ray Crystallography.
Authors: Fukuda, Y. / Lintuluoto, M. / Kurihara, K. / Hasegawa, K. / Inoue, T. / Tamada, T.
History
DepositionAug 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8323
Polymers13,6731
Non-polymers1602
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-13 kcal/mol
Surface area6600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.676, 49.676, 96.519
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
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,z+1/2

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Components

#1: Protein Pseudoazurin / Blue copper protein / Cupredoxin


Mass: 13672.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Strain: S-6 / Plasmid: pET24-c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04377
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.35 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Feb 14, 2022
Details: DECTRIS EIGER2 X CdTe 4M was used for data collection
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.35 Å / Relative weight: 1
ReflectionResolution: 0.86→43.02 Å / Num. obs: 113729 / % possible obs: 99.7 % / Redundancy: 10.4 % / Biso Wilson estimate: 8.77 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.024 / Net I/σ(I): 16.3
Reflection shellResolution: 0.86→0.87 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.818 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5638 / CC1/2: 0.519 / Rpim(I) all: 0.594 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.86→24.05 Å / SU ML: 0.0766 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.2438
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1625 5708 5.02 %
Rwork0.144 107919 -
obs0.1449 113627 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.98 Å2
Refinement stepCycle: LAST / Resolution: 0.86→24.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 6 276 1229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681343
X-RAY DIFFRACTIONf_angle_d1.28361847
X-RAY DIFFRACTIONf_chiral_restr0.0821207
X-RAY DIFFRACTIONf_plane_restr0.0078249
X-RAY DIFFRACTIONf_dihedral_angle_d14.533525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.86-0.870.28792140.27963584X-RAY DIFFRACTION99.97
0.87-0.880.27791720.27243597X-RAY DIFFRACTION99.97
0.88-0.890.29182100.26313575X-RAY DIFFRACTION99.97
0.89-0.90.25431870.24813630X-RAY DIFFRACTION100
0.9-0.910.24471920.2353555X-RAY DIFFRACTION100
0.91-0.930.24451790.23393636X-RAY DIFFRACTION99.97
0.93-0.940.26822370.22433570X-RAY DIFFRACTION100
0.94-0.950.22351950.20923630X-RAY DIFFRACTION100
0.95-0.970.2372150.19883518X-RAY DIFFRACTION100
0.97-0.980.20591940.19943600X-RAY DIFFRACTION100
0.98-10.19442170.18643604X-RAY DIFFRACTION100
1-1.020.21931770.17093586X-RAY DIFFRACTION99.95
1.02-1.040.18071970.16453613X-RAY DIFFRACTION99.97
1.04-1.060.17711900.15823631X-RAY DIFFRACTION100
1.06-1.080.17231670.15053603X-RAY DIFFRACTION100
1.08-1.110.14751780.15093612X-RAY DIFFRACTION100
1.11-1.140.16171810.14353577X-RAY DIFFRACTION100
1.14-1.170.16851840.14293651X-RAY DIFFRACTION100
1.17-1.20.15151940.14413579X-RAY DIFFRACTION100
1.2-1.240.1781850.14013638X-RAY DIFFRACTION99.97
1.24-1.280.15121920.14533590X-RAY DIFFRACTION100
1.28-1.340.16571930.14223601X-RAY DIFFRACTION100
1.34-1.40.15192010.13813608X-RAY DIFFRACTION100
1.4-1.470.15631920.13433621X-RAY DIFFRACTION100
1.47-1.560.13731920.12733591X-RAY DIFFRACTION100
1.56-1.680.14931840.12793621X-RAY DIFFRACTION100
1.68-1.850.14871870.13093647X-RAY DIFFRACTION100
1.85-2.120.14091350.12293671X-RAY DIFFRACTION100
2.12-2.670.12851680.12193638X-RAY DIFFRACTION100
2.67-24.050.16491990.14223342X-RAY DIFFRACTION91.81

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