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- PDB-7dvh: Crystal structure of the computationally designed reDPBB_sym4 protein -

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Basic information

Entry
Database: PDB / ID: 7dvh
TitleCrystal structure of the computationally designed reDPBB_sym4 protein
ComponentsreDPBB_sym4 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: 1.698 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 1.0Sep 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: reDPBB_sym4 protein
B: reDPBB_sym4 protein
D: reDPBB_sym4 protein
C: reDPBB_sym4 protein


Theoretical massNumber of molelcules
Total (without water)39,3294
Polymers39,3294
Non-polymers00
Water5,891327
1
A: reDPBB_sym4 protein


Theoretical massNumber of molelcules
Total (without water)9,8321
Polymers9,8321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: reDPBB_sym4 protein


Theoretical massNumber of molelcules
Total (without water)9,8321
Polymers9,8321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: reDPBB_sym4 protein


Theoretical massNumber of molelcules
Total (without water)9,8321
Polymers9,8321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: reDPBB_sym4 protein


Theoretical massNumber of molelcules
Total (without water)9,8321
Polymers9,8321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.909, 30.467, 93.422
Angle α, β, γ (deg.)90.000, 101.590, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11B-154-

HOH

21D-106-

HOH

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Components

#1: Protein
reDPBB_sym4 protein


Mass: 9832.351 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)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200mM Sodium citrate tribasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.698→50 Å / Num. obs: 40180 / % possible obs: 99.6 % / Redundancy: 6.59 % / CC1/2: 0.99 / Net I/σ(I): 20.25
Reflection shellResolution: 1.698→1.8 Å / Num. unique obs: 6345 / CC1/2: 0.937

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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: 1.698→47.905 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 19.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 1998 4.97 %
Rwork0.1813 38176 -
obs0.1823 40174 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.12 Å2 / Biso mean: 26.3131 Å2 / Biso min: 11.12 Å2
Refinement stepCycle: final / Resolution: 1.698→47.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 0 327 3025
Biso mean---36.94 -
Num. residues----355
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.698-1.74010.28091340.2358257097
1.7401-1.78720.28381450.22422752100
1.7872-1.83980.2191400.21222674100
1.8398-1.89910.24351410.20122716100
1.8991-1.9670.25411420.1881268699
1.967-2.04580.21231430.19042718100
2.0458-2.13890.22351410.18352693100
2.1389-2.25170.20051410.18452722100
2.2517-2.39270.19971430.18872736100
2.3927-2.57750.23551440.19242734100
2.5775-2.83680.20261440.18452761100
2.8368-3.24720.18291430.17312745100
3.2472-4.09080.1751460.15672779100
4.0908-47.9050.17491510.17292890100

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