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- PDB-8jvz: Crystal structure of the circular-permutated protein mkaL2_v1_SH3 -

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Basic information

Entry
Database: PDB / ID: 8jvz
TitleCrystal structure of the circular-permutated protein mkaL2_v1_SH3
ComponentsmkaL2_v1_SH3
KeywordsRIBOSOMAL PROTEIN / SH3 fold
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsYagi, S. / Tagami, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H01328 Japan
Japan Society for the Promotion of Science (JSPS)20K15854 Japan
Japan Society for the Promotion of Science (JSPS)22H01346 Japan
CitationJournal: Nat Commun / Year: 2024
Title: An ancestral fold reveals the evolutionary link between RNA polymerase and ribosomal proteins.
Authors: Yagi, S. / Tagami, S.
History
DepositionJun 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mkaL2_v1_SH3
B: mkaL2_v1_SH3


Theoretical massNumber of molelcules
Total (without water)11,5952
Polymers11,5952
Non-polymers00
Water1,928107
1
A: mkaL2_v1_SH3


Theoretical massNumber of molelcules
Total (without water)5,7981
Polymers5,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mkaL2_v1_SH3


Theoretical massNumber of molelcules
Total (without water)5,7981
Polymers5,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.182, 28.280, 38.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-106-

HOH

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Components

#1: Protein mkaL2_v1_SH3


Mass: 5797.727 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.: 107 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% 2-propanol, 100mM Tris-HCl pH8.5, 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.892→50 Å / Num. obs: 15179 / % possible obs: 99.2 % / Redundancy: 3.4 % / CC1/2: 0.99 / Net I/σ(I): 9.97
Reflection shellResolution: 1.892→2 Å / Num. unique obs: 2445 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.892→38.768 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 1517 9.99 %
Rwork0.2188 --
obs0.2205 15178 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.892→38.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms774 0 0 107 881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013782
X-RAY DIFFRACTIONf_angle_d1.4781054
X-RAY DIFFRACTIONf_dihedral_angle_d28.97308
X-RAY DIFFRACTIONf_chiral_restr0.463126
X-RAY DIFFRACTIONf_plane_restr0.006138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8924-1.95350.30231350.30361193X-RAY DIFFRACTION97
1.9535-2.02330.26021440.26011300X-RAY DIFFRACTION100
2.0233-2.10430.29611300.25471201X-RAY DIFFRACTION100
2.1043-2.20.25371390.23471267X-RAY DIFFRACTION100
2.2-2.3160.33531400.25041232X-RAY DIFFRACTION99
2.316-2.46110.26771350.25921244X-RAY DIFFRACTION100
2.4611-2.65110.2921380.26311252X-RAY DIFFRACTION99
2.6511-2.91780.30541410.25311241X-RAY DIFFRACTION99
2.9178-3.33980.22761330.22971229X-RAY DIFFRACTION99
3.3398-4.2070.18811450.1841247X-RAY DIFFRACTION100
4.207-38.7680.18371370.17661255X-RAY DIFFRACTION99

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