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- PDB-7dvf: Crystal structure of the computationally designed reDPBB_sym2 protein -

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Basic information

Entry
Database: PDB / ID: 7dvf
TitleCrystal structure of the computationally designed reDPBB_sym2 protein
ComponentsreDPBB_sym2 protein
KeywordsCHAPERONE / Double psi beta barrel
Function / homologyBarwin-like endoglucanases - #20 / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.209 Å
AuthorsYagi, S. / Tagami, S. / Padhi, A.K. / Zhang, K.Y.J.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H01328 Japan
CitationJournal: 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.
History
DepositionJan 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: reDPBB_sym2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5362
Polymers9,4181
Non-polymers1181
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-6 kcal/mol
Surface area4820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.280, 33.536, 79.184
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 reDPBB_sym2 protein


Mass: 9418.103 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)
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 1.85 Å3/Da / Density % sol: 33.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM Sodium acetate pH6.2, 35% MPD, 20% PEG1500

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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: Apr 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 21779 / % possible obs: 98.6 % / Redundancy: 12.1 % / CC1/2: 0.999 / Net I/σ(I): 29.03
Reflection shellResolution: 1.21→1.28 Å / Num. unique obs: 2768 / CC1/2: 0.995

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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: 1.209→21.896 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 17.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1953 2000 9.18 %
Rwork0.1536 19775 -
obs0.1573 21775 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.93 Å2 / Biso mean: 22.1422 Å2 / Biso min: 4.13 Å2
Refinement stepCycle: final / Resolution: 1.209→21.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms642 0 8 122 772
Biso mean--22.95 38.75 -
Num. residues----84
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.209-1.23920.28241300.267127891
1.2392-1.27270.27651390.2672137798
1.2727-1.31010.24531430.26291420100
1.3101-1.35240.19741430.16211400100
1.3524-1.40080.19131440.13731429100
1.4008-1.45680.20341440.14611426100
1.4568-1.52310.20471440.14981422100
1.5231-1.60340.16041420.12391411100
1.6034-1.70380.16811440.13351426100
1.7038-1.83530.16681460.13611446100
1.8353-2.01990.18591460.13931444100
2.0199-2.31190.16011470.13311449100
2.3119-2.91170.20141490.1541477100
2.9117-21.8960.22681390.1675137087

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