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- PDB-7du6: Crystal structure of the rationally designed mkDPBB_sym2 protein -

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Basic information

Entry
Database: PDB / ID: 7du6
TitleCrystal structure of the rationally designed mkDPBB_sym2 protein
ComponentsmkDPBB_sym2 protein
KeywordsCHAPERONE / Double psi beta barrel
Function / homologyBarwin-like endoglucanases - #20 / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYagi, S. / Tagami, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H01328 Japan
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase.
Authors: Yagi, S. / Padhi, A.K. / Vucinic, J. / Barbe, S. / Schiex, T. / Nakagawa, R. / Simoncini, D. / Zhang, K.Y.J. / Tagami, S.
History
DepositionJan 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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: mkDPBB_sym2 protein


Theoretical massNumber of molelcules
Total (without water)10,1191
Polymers10,1191
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4970 Å2
Unit cell
Length a, b, c (Å)70.891, 70.891, 64.045
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-116-

HOH

21A-184-

HOH

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Components

#1: Protein mkDPBB_sym2 protein


Mass: 10118.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 100mM CHES pH 9.5, 1M sodium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 15809 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 1 / Net I/σ(I): 32.34
Reflection shellResolution: 1.6→1.7 Å / Num. unique obs: 2522 / CC1/2: 0.883

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DG7

7dg7


Resolution: 1.6→44.319 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 2.05 / Phase error: 23.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 1574 9.96 %
Rwork0.194 14232 -
obs0.1954 15806 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.34 Å2 / Biso mean: 32.0494 Å2 / Biso min: 17.26 Å2
Refinement stepCycle: final / Resolution: 1.6→44.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms678 0 0 85 763
Biso mean---37.67 -
Num. residues----86
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6003-1.6520.28391420.2808128399
1.652-1.7110.34431410.2721286100
1.711-1.77950.25831430.25021301100
1.7795-1.86050.26011400.2451283100
1.8605-1.95860.24831400.23751299100
1.9586-2.08130.22591470.21741309100
2.0813-2.2420.24551390.19841272100
2.242-2.46760.21561450.2051323100
2.4676-2.82460.24271420.19711292100
2.8246-3.55850.18331480.17711301100
3.5585-44.3190.16971470.16821283100

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