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- PDB-7dxv: Crystal structure of the mk2h_deltaY peptide homodimer -

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Basic information

Entry
Database: PDB / ID: 7dxv
TitleCrystal structure of the mk2h_deltaY peptide homodimer
Componentsmk2h_dY protein
KeywordsCHAPERONE / Double psi beta barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsYagi, S. / Tagami, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H01328 Japan
Citation
Journal: 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.
#1: Journal: Biorxiv / Year: 2021
Title: Seven amino acid types suffice to reconstruct 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 20, 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
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: mk2h_dY protein
A: mk2h_dY protein


Theoretical massNumber of molelcules
Total (without water)10,2522
Polymers10,2522
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-17 kcal/mol
Surface area5120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.101, 73.101, 49.177
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-118-

HOH

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Components

#1: Protein/peptide mk2h_dY protein


Mass: 5126.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM SPG buffer, 25 % PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 4833 / % possible obs: 98 % / Redundancy: 10.87 % / CC1/2: 0.999 / Net I/σ(I): 29.72
Reflection shellResolution: 2.21→2.34 Å / Num. unique obs: 705 / CC1/2: 0.993

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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: 7DXR

7dxr


Resolution: 2.301→36.551 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 2.33 / Phase error: 30.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 441 10.12 %
Rwork0.2016 3915 -
obs0.2061 4356 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.95 Å2 / Biso mean: 41.5106 Å2 / Biso min: 15.35 Å2
Refinement stepCycle: final / Resolution: 2.301→36.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms654 0 0 34 688
Biso mean---40.36 -
Num. residues----86
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.301-2.63350.35321440.27391304
2.6335-3.31750.25871490.23261314
3.3175-36.5510.2191480.17071297

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