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- PDB-7dxt: Crystal structure of the chemically synthesized mk2h peptide homodimer -

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Basic information

Entry
Database: PDB / ID: 7dxt
TitleCrystal structure of the chemically synthesized mk2h peptide homodimer
Componentsmk2h protein
KeywordsCHAPERONE / Double psi beta barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
A: mk2h protein


Theoretical massNumber of molelcules
Total (without water)5,2881
Polymers5,2881
Non-polymers00
Water82946
1
A: mk2h protein

A: mk2h protein


Theoretical massNumber of molelcules
Total (without water)10,5762
Polymers10,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-11
Buried area4230 Å2
ΔGint-23 kcal/mol
Surface area5120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.151, 70.151, 65.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-110-

HOH

21A-116-

HOH

31A-130-

HOH

41A-131-

HOH

51A-141-

HOH

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Components

#1: Protein/peptide mk2h protein


Mass: 5288.193 Da / Num. of mol.: 1
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.: 46 / 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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 800mM Sodium phosphate monobasic/1200mM Pottasium phosphate dibasic, 100 mM Sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 5895 / % possible obs: 100 % / Redundancy: 19.72 % / CC1/2: 1 / Net I/σ(I): 33.39
Reflection shellResolution: 1.8→1.91 Å / Num. unique obs: 938 / CC1/2: 0.934

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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: 7DU6

7du6


Resolution: 1.8→35.075 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 588 9.98 %
Rwork0.1853 5303 -
obs0.1878 5891 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.14 Å2 / Biso mean: 36.7289 Å2 / Biso min: 17.53 Å2
Refinement stepCycle: final / Resolution: 1.8→35.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms340 0 0 46 386
Biso mean---47.21 -
Num. residues----43
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8-1.9790.26511450.27471302
1.979-2.26540.25131440.19961311
2.2654-2.85390.22551460.19121312
2.8539-35.0750.191530.16871378

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