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- PDB-8jvq: Crystal structure of the dimeric RIFT fold protein Ph1_DG -

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Basic information

Entry
Database: PDB / ID: 8jvq
TitleCrystal structure of the dimeric RIFT fold protein Ph1_DG
ComponentsPh1_DG
KeywordsDNA BINDING PROTEIN / RIFT barrel
Function / homologyCITRIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 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: Ph1_DG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9703
Polymers4,6821
Non-polymers2882
Water72140
1
A: Ph1_DG
hetero molecules

A: Ph1_DG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9406
Polymers9,3632
Non-polymers5764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3980 Å2
ΔGint-43 kcal/mol
Surface area6030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.017, 35.017, 54.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-233-

HOH

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Components

#1: Protein/peptide Ph1_DG


Mass: 4681.695 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 3200mM Ammonium sulfate, 100mM Citric acid/Sodium hydroxide pH5.0

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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 MX-225 / Detector: CCD / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 14659 / % possible obs: 99.2 % / Redundancy: 11.1 % / CC1/2: 1 / Net I/σ(I): 12.45
Reflection shellResolution: 1.4→1.5 Å / Num. unique obs: 2362 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.401→26.518 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 674 4.6 %
Rwork0.2122 --
obs0.2135 14649 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.401→26.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms328 0 18 40 386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017355
X-RAY DIFFRACTIONf_angle_d1.28478
X-RAY DIFFRACTIONf_dihedral_angle_d26.488142
X-RAY DIFFRACTIONf_chiral_restr0.09254
X-RAY DIFFRACTIONf_plane_restr0.00661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4012-1.50940.26581190.26352849X-RAY DIFFRACTION100
1.5094-1.66130.24731270.26592809X-RAY DIFFRACTION100
1.6613-1.90160.30931560.26892760X-RAY DIFFRACTION100
1.9016-2.39560.21611380.2162819X-RAY DIFFRACTION100
2.3956-26.5180.23081340.18672738X-RAY DIFFRACTION97

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