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- PDB-7du7: Crystal structure of the rationally designed mkDPBB_sym1 protein -

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Basic information

Entry
Database: PDB / ID: 7du7
TitleCrystal structure of the rationally designed mkDPBB_sym1 protein
ComponentsmkDPBB_sym1 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: 1.201 Å
AuthorsYagi, S. / Tagami, S.
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 8, 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
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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: mkDPBB_sym1 protein
B: mkDPBB_sym1 protein


Theoretical massNumber of molelcules
Total (without water)19,5252
Polymers19,5252
Non-polymers00
Water2,252125
1
A: mkDPBB_sym1 protein


Theoretical massNumber of molelcules
Total (without water)9,7631
Polymers9,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mkDPBB_sym1 protein


Theoretical massNumber of molelcules
Total (without water)9,7631
Polymers9,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.259, 31.259, 132.177
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein mkDPBB_sym1 protein


Mass: 9762.511 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)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.91 Å3/Da / Density % sol: 35.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2100mM Maleic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 29, 2019
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: 44946 / % possible obs: 99.7 % / Redundancy: 4.88 % / CC1/2: 0.999 / Net I/σ(I): 16.14
Reflection shellResolution: 1.2→1.27 Å / Num. unique obs: 7142 / CC1/2: 0.9915

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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: 1.201→27.071 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 2.06 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 2027 4.52 %
Rwork0.2038 42865 -
obs0.2045 44892 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.07 Å2 / Biso mean: 26.9676 Å2 / Biso min: 11.44 Å2
Refinement stepCycle: final / Resolution: 1.201→27.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 0 125 1429
Biso mean---38.65 -
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 (%)
1.201-1.23060.28991450.3226295997
1.2306-1.26390.31161460.30093025100
1.2639-1.30110.35851470.29973129100
1.3011-1.3430.30191480.27053010100
1.343-1.3910.32141440.24983094100
1.391-1.44670.23481380.24633069100
1.4467-1.51260.28161440.23063086100
1.5126-1.59230.22981380.23043111100
1.5923-1.69210.25451400.23213057100
1.6921-1.82270.22161390.21663080100
1.8227-2.00610.21191440.19943063100
2.0061-2.29620.22571520.19713095100
2.2962-2.89240.20081540.19663048100
2.8924-27.0710.1931480.1777303999

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