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- PDB-6l9s: Crystal structure of Na-dithionite reduced auracyanin from photos... -

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Basic information

Entry
Database: PDB / ID: 6l9s
TitleCrystal structure of Na-dithionite reduced auracyanin from photosynthetic bacterium Roseiflexus castenholzii
ComponentsBlue (Type 1) copper domain protein
KeywordsMETAL BINDING PROTEIN / Auracyanin / Roseiflexus castenholzii / Electron transfer / Na-dithionite reduced / Blue copper protein
Function / homology
Function and homology information


electron transfer activity / copper ion binding
Similarity search - Function
Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (I) ION / Blue (Type 1) copper domain protein
Similarity search - Component
Biological speciesRoseiflexus castenholzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, C. / Zhang, C.Y. / Min, Z.Z. / Xu, X.L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570738 China
National Natural Science Foundation of China31870740 China
National Natural Science Foundation of China31400630 China
CitationJournal: Photosyn. Res. / Year: 2020
Title: Structural basis underlying the electron transfer features of a blue copper protein auracyanin from the photosynthetic bacterium Roseiflexus castenholzii.
Authors: Wang, C. / Xin, Y. / Min, Z. / Qi, J. / Zhang, C. / Xu, X.
History
DepositionNov 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 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 / _citation_author.name
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: Blue (Type 1) copper domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2652
Polymers13,2021
Non-polymers641
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The absorption peak of auracyanin in gel filtration is corresponding to a monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.989, 57.420, 65.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

21A-359-

HOH

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Components

#1: Protein Blue (Type 1) copper domain protein / auracyanin


Mass: 13201.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
References: UniProt: A7NNM5
#2: Chemical ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.3M Sodium citrate, 0.05M Tris-Cl, adding 0.3M Na-dithionite in the crystal drop of air-oxidized auracyanin to obtain the reduced crystals

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→43.08 Å / Num. obs: 8318 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 20.04 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.04 / Rrim(I) all: 0.099 / Χ2: 0.582 / Net I/σ(I): 15.23
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 4.2 / Num. unique obs: 396 / CC1/2: 0.941 / Rpim(I) all: 0.158 / Rrim(I) all: 0.382 / Χ2: 0.741 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KOL

6kol


Resolution: 2→43.08 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.941 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 398 4.8 %RANDOM
Rwork0.1773 ---
obs0.1793 7889 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 41.98 Å2 / Biso mean: 21.685 Å2 / Biso min: 14.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.62 Å20 Å2-0 Å2
2---1.55 Å20 Å2
3----1.07 Å2
Refinement stepCycle: final / Resolution: 2→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 1 76 987
Biso mean--19.68 27.19 -
Num. residues----125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.014929
X-RAY DIFFRACTIONr_bond_other_d0.0010.017850
X-RAY DIFFRACTIONr_angle_refined_deg0.9231.6731268
X-RAY DIFFRACTIONr_angle_other_deg0.8041.641988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5375124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.16325.58834
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26315139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.019151
X-RAY DIFFRACTIONr_chiral_restr0.040.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021043
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02161
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.261 37 -
Rwork0.187 548 -
obs--95.43 %

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