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- PDB-6l1v: Domain-swapped Alcaligenes xylosoxidans azurin dimer -

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Basic information

Entry
Database: PDB / ID: 6l1v
TitleDomain-swapped Alcaligenes xylosoxidans azurin dimer
ComponentsAzurin-1
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion 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-1
Similarity search - Component
Biological speciesAlcaligenes xylosoxydans xylosoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCahyono, R.N. / Yamanaka, M. / Nagao, S. / Shibata, N. / Higuchi, Y. / Hirota, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP18H02088 Japan
Japan Society for the Promotion of ScienceJP16K17935 Japan
Japan Society for the Promotion of ScienceJP19K05695 Japan
CitationJournal: Metallomics / Year: 2020
Title: 3D domain swapping of azurin from Alcaligenes xylosoxidans.
Authors: Cahyono, R.N. / Yamanaka, M. / Nagao, S. / Shibata, N. / Higuchi, Y. / Hirota, S.
History
DepositionSep 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Azurin-1
C: Azurin-1
E: Azurin-1
G: Azurin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1548
Polymers55,9004
Non-polymers2544
Water4,846269
1
A: Azurin-1
G: Azurin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0774
Polymers27,9502
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-35 kcal/mol
Surface area13020 Å2
MethodPISA
2
C: Azurin-1
E: Azurin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0774
Polymers27,9502
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-36 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.451, 167.809, 116.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Azurin-1 / AZN-1 / Azurin-I


Mass: 13974.933 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes xylosoxydans xylosoxydans (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P56547
#2: Chemical
ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 269 / 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: 4.72 Å3/Da / Density % sol: 73.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES-NaOH, 25% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→49.17 Å / Num. obs: 50385 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.3
Reflection shellResolution: 2.25→2.32 Å / Rmerge(I) obs: 1.145 / Num. unique obs: 4598 / CC1/2: 0.739

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RKR

1rkr


Resolution: 2.25→49.17 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.23021 2534 -
Rwork0.20277 --
obs0.20414 47826 99.9 %
Refinement stepCycle: LAST / Resolution: 2.25→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3908 0 4 269 4181
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 199 -
Rwork0.327 3450 -
obs--100 %

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