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- PDB-7dxw: Crystal structure of the mk2h_deltaMIL peptide homodimer -

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Basic information

Entry
Database: PDB / ID: 7dxw
TitleCrystal structure of the mk2h_deltaMIL peptide homodimer
Componentsmk2h_deltaMIL protein
KeywordsCHAPERONE / Double psi beta barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.509 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_deltaMIL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3242
Polymers5,2281
Non-polymers961
Water1,11762
1
A: mk2h_deltaMIL protein
hetero molecules

A: mk2h_deltaMIL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6484
Polymers10,4562
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area4600 Å2
ΔGint-47 kcal/mol
Surface area5170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.596, 69.596, 65.781
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-202-

HOH

21A-245-

HOH

31A-251-

HOH

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Components

#1: Protein/peptide mk2h_deltaMIL protein


Mass: 5228.074 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Imidazole Hydrochloric acid pH 8.0, 200 mM Lithium sulfate, 10% PEG 3000

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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 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 9804 / % possible obs: 99.9 % / Redundancy: 21.62 % / CC1/2: 0.998 / Net I/σ(I): 23.33
Reflection shellResolution: 1.5→1.6 Å / Num. unique obs: 1557 / CC1/2: 0.945

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DXR

7dxr


Resolution: 1.509→34.798 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 981 10.01 %
Rwork0.1816 8822 -
obs0.1831 9803 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.79 Å2 / Biso mean: 25.1147 Å2 / Biso min: 10.4 Å2
Refinement stepCycle: final / Resolution: 1.509→34.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms337 0 5 62 404
Biso mean--64.3 38.25 -
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
1.5092-1.58870.24581370.25911233
1.5887-1.68830.25321390.22121248
1.6883-1.81860.22111380.20131245
1.8186-2.00160.19931390.19461256
2.0016-2.29120.20641400.18181261
2.2912-2.88640.22131410.16711265
2.8864-34.7980.16731470.17161314

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