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- PDB-7dxu: Crystal structure of the mk2h_deltaP peptide homodimer -

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Basic information

Entry
Database: PDB / ID: 7dxu
TitleCrystal structure of the mk2h_deltaP peptide homodimer
Componentsmk2h_dP protein
KeywordsCHAPERONE / Double psi beta barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.314 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_dP protein
A: mk2h_dP protein
C: mk2h_dP protein
D: mk2h_dP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,62510
Polymers21,0494
Non-polymers5766
Water1,35175
1
B: mk2h_dP protein
A: mk2h_dP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8135
Polymers10,5242
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-70 kcal/mol
Surface area4860 Å2
MethodPISA
2
C: mk2h_dP protein
D: mk2h_dP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8135
Polymers10,5242
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-62 kcal/mol
Surface area4910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.476, 55.892, 56.423
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_dP protein


Mass: 5262.156 Da / Num. of mol.: 4
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2000 mM Ammonium sulfate, 100 mM CAPS/ Sodium hydroxide, pH 10.5, 200 mM Lithium sulfate

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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: 2.3→50 Å / Num. obs: 7930 / % possible obs: 99.4 % / Redundancy: 13.42 % / CC1/2: 1 / Net I/σ(I): 54.21
Reflection shellResolution: 2.3→2.45 Å / Num. unique obs: 1264 / CC1/2: 1

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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: 2.314→39.191 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2646 791 9.99 %
Rwork0.2569 7128 -
obs0.2576 7919 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.45 Å2 / Biso mean: 26.9839 Å2 / Biso min: 7.56 Å2
Refinement stepCycle: final / Resolution: 2.314→39.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 30 75 1457
Biso mean--29.03 26.98 -
Num. residues----172
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.314-2.4590.28761240.28931169
2.459-2.64880.2991310.3121156
2.6488-2.91530.28961320.30841178
2.9153-3.3370.22681310.28181165
3.337-4.20340.24941350.22911199
4.2034-39.1910.27461380.21871261

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