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- PDB-7dxy: Crystal structure of the chemically synthesized mk2h_deltaMILPS p... -

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Basic information

Entry
Database: PDB / ID: 7dxy
TitleCrystal structure of the chemically synthesized mk2h_deltaMILPS peptide homodimer
Componentsmk2h_deltaMILPS
KeywordsCHAPERONE / Double psi beta barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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

Downloads & links

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Assembly

Deposited unit
B: mk2h_deltaMILPS
A: mk2h_deltaMILPS


Theoretical massNumber of molelcules
Total (without water)9,6932
Polymers9,6932
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-17 kcal/mol
Surface area4720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.660, 39.688, 64.283
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide mk2h_deltaMILPS


Mass: 4846.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 400mM Sodium phosphate monobasic/1600mM Pottasium phosphate dibasic, 100 mM imidazole_HCl, pH 8.0, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 17566 / % possible obs: 99.2 % / Redundancy: 6.26 % / CC1/2: 1 / Net I/σ(I): 18.85
Reflection shellResolution: 1.35→1.44 Å / Num. unique obs: 2759 / CC1/2: 0.832

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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: 7DXX

7dxx


Resolution: 1.4→24.263 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 29.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 1592 10.02 %
Rwork0.211 14304 -
obs0.2129 15896 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.94 Å2 / Biso mean: 31.1788 Å2 / Biso min: 16.93 Å2
Refinement stepCycle: final / Resolution: 1.4→24.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms664 0 0 96 760
Biso mean---40.46 -
Num. residues----84
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.44520.31841390.32571253100
1.4452-1.49680.29581440.29611286100
1.4968-1.55680.28211430.27631288100
1.5568-1.62760.2441420.25591292100
1.6276-1.71340.29871440.2542129199
1.7134-1.82070.23631440.2355128599
1.8207-1.96120.22171420.23128499
1.9612-2.15850.18841470.19761322100
2.1585-2.47050.24651450.1961131199
2.4705-3.11160.21371500.2111336100
3.1116-24.2630.22271520.1908135695

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