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- PDB-7dxx: Crystal structure of the mk2h_deltaMILPS peptide homodimer -

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Basic information

Entry
Database: PDB / ID: 7dxx
TitleCrystal structure of the mk2h_deltaMILPS peptide homodimer
Componentsmk2h_deltaMILPS protein
KeywordsCHAPERONE / Double psi beta barrel
Function / homologyMALONIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.403 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_deltaMILPS protein
A: mk2h_deltaMILPS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6773
Polymers10,5722
Non-polymers1041
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-22 kcal/mol
Surface area5420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.761, 33.761, 148.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-174-

HOH

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Components

#1: Protein/peptide mk2h_deltaMILPS protein


Mass: 5286.242 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: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2000 M Sodium malonate dibasic

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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: 1.4→50 Å / Num. obs: 17646 / % possible obs: 99.3 % / Redundancy: 11.73 % / CC1/2: 0.999 / Net I/σ(I): 29.38
Reflection shellResolution: 1.4→1.49 Å / Num. unique obs: 2652 / CC1/2: 0.94

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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: 7DXW

7dxw


Resolution: 1.403→37.053 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2001 1764 10 %
Rwork0.1838 15882 -
obs0.1854 17646 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.26 Å2 / Biso mean: 21.5126 Å2 / Biso min: 8.01 Å2
Refinement stepCycle: final / Resolution: 1.403→37.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms705 0 7 141 853
Biso mean--19.3 33.05 -
Num. residues----90
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4032-1.44110.32181200.2466108293
1.4411-1.48350.24221330.2253118999
1.4835-1.53140.22691320.20231193100
1.5314-1.58610.20671330.18721196100
1.5861-1.64960.24051340.19481202100
1.6496-1.72470.22271330.20421213100
1.7247-1.81560.24471340.20261199100
1.8156-1.92940.19881350.18951221100
1.9294-2.07830.18531390.181240100
2.0783-2.28750.19581360.17251235100
2.2875-2.61840.18561390.1761247100
2.6184-3.29860.17661410.17621274100
3.2986-37.0530.19571550.17731391100

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