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- PDB-7dxr: Crystal structure of the mk2h peptide homodimer. -

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Basic information

Entry
Database: PDB / ID: 7dxr
TitleCrystal structure of the mk2h peptide homodimer.
Componentsmk2h protein
KeywordsCHAPERONE / Double psi beta barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
A: mk2h protein
B: mk2h protein
C: mk2h protein
D: mk2h protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,85410
Polymers21,1534
Non-polymers7026
Water2,144119
1
A: mk2h protein
B: mk2h protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8655
Polymers10,5762
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-71 kcal/mol
Surface area5300 Å2
MethodPISA
2
C: mk2h protein
D: mk2h protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9905
Polymers10,5762
Non-polymers4133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-51 kcal/mol
Surface area4830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.114, 56.031, 56.541
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 protein


Mass: 5288.193 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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1200mM Sodium phosphate monobasic/800mM Pottasium phosphate dibasic, 100 mM CAPS pH 10.5, 100mM 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: Jan 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 23802 / % possible obs: 99.9 % / Redundancy: 11.11 % / CC1/2: 1 / Net I/σ(I): 25.31
Reflection shellResolution: 1.6→1.69 Å / Num. unique obs: 3762 / CC1/2: 0.899

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DU6

7du6


Resolution: 1.6→39.8 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 2009 8.45 %
Rwork0.2137 21779 -
obs0.2166 23788 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.5 Å2 / Biso mean: 29.7405 Å2 / Biso min: 12.02 Å2
Refinement stepCycle: final / Resolution: 1.6→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 39 119 1539
Biso mean--32.8 37.67 -
Num. residues----176
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.35381460.28471517166398
1.64-1.680.37121450.283814991644100
1.68-1.730.2961430.268415361679100
1.73-1.790.27891400.246915431683100
1.79-1.850.2911370.241415391676100
1.85-1.930.34821380.251415351673100
1.93-2.010.31341360.225515591695100
2.01-2.120.25661400.222815371677100
2.12-2.250.28921510.218815501701100
2.25-2.430.26771440.228215491693100
2.43-2.670.28381370.22915691706100
2.67-3.060.25841510.215115711722100
3.06-3.850.20931470.18615841731100
3.85-39.80.19841540.194116911845100

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