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- PDB-7dww: Crystal structure of the computationally designed msDPBB_sym2 protein -

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Basic information

Entry
Database: PDB / ID: 7dww
TitleCrystal structure of the computationally designed msDPBB_sym2 protein
ComponentsmsDPBB_sym2 protein
KeywordsCHAPERONE / Double psi beta barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsYagi, S. / Schiex, T. / Vucinic, J. / Barbe, S. / Simoncini, D. / 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 18, 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: msDPBB_sym2 protein
A: msDPBB_sym2 protein


Theoretical massNumber of molelcules
Total (without water)19,2992
Polymers19,2992
Non-polymers00
Water2,162120
1
B: msDPBB_sym2 protein


Theoretical massNumber of molelcules
Total (without water)9,6491
Polymers9,6491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: msDPBB_sym2 protein


Theoretical massNumber of molelcules
Total (without water)9,6491
Polymers9,6491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.864, 44.864, 147.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein msDPBB_sym2 protein


Mass: 9649.415 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM CAPS pH10.5, 2M Ammonium sulfate, 200 mM Lithium sulfate

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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: 1.8→50 Å / Num. obs: 16713 / % possible obs: 99.9 % / Redundancy: 9.45 % / CC1/2: 0.999 / Net I/σ(I): 12.76
Reflection shellResolution: 1.8→1.91 Å / Num. unique obs: 2581 / CC1/2: 0.763

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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: 1.802→38.853 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 1684 10.08 %
Rwork0.2329 15028 -
obs0.2344 16712 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.79 Å2 / Biso mean: 46.7414 Å2 / Biso min: 22.43 Å2
Refinement stepCycle: final / Resolution: 1.802→38.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 0 120 1436
Biso mean---45.42 -
Num. residues----172
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8021-1.85510.34731400.3207120999
1.8551-1.9150.31021280.30461200100
1.915-1.98340.32981390.31031225100
1.9834-2.06280.24251380.27261244100
2.0628-2.15670.31521380.26571238100
2.1567-2.27040.23621370.2551223100
2.2704-2.41260.27331370.24761249100
2.4126-2.59890.23551420.25211250100
2.5989-2.86040.24781410.25551250100
2.8604-3.27410.2531430.22891273100
3.2741-4.12430.21661450.20521288100
4.1243-38.8530.23851560.21121379100

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