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- PDB-8jvp: Crystal structure of the dimeric DZBB fold protein Ph1 -

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Basic information

Entry
Database: PDB / ID: 8jvp
TitleCrystal structure of the dimeric DZBB fold protein Ph1
ComponentsPh1
KeywordsDNA BINDING PROTEIN / Double zeta beta barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.302 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2342
Polymers5,1381
Non-polymers961
Water84747
1
A: Ph1
hetero molecules

A: Ph1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4694
Polymers10,2762
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3950 Å2
ΔGint-49 kcal/mol
Surface area5820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.056, 35.056, 54.844
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-211-

HOH

21A-237-

HOH

31A-246-

HOH

41A-247-

HOH

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Components

#1: Protein/peptide Ph1


Mass: 5138.210 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.89 Å3/Da / Density % sol: 35.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 400, 100mM Tris pH8.0, 400mM Lithium sulfate

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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: Jan 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 18226 / % possible obs: 98.7 % / Redundancy: 18.2 % / CC1/2: 1 / Net I/σ(I): 0.42
Reflection shellResolution: 1.3→1.38 Å / Num. unique obs: 31946 / 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: 1.302→20.35 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 1869 10.25 %
Rwork0.1897 --
obs0.1933 18226 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.302→20.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms360 0 5 47 412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012385
X-RAY DIFFRACTIONf_angle_d1.205519
X-RAY DIFFRACTIONf_dihedral_angle_d25.672155
X-RAY DIFFRACTIONf_chiral_restr0.08260
X-RAY DIFFRACTIONf_plane_restr0.00767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3022-1.33740.28571380.2421234X-RAY DIFFRACTION98
1.3374-1.37680.31121480.21131270X-RAY DIFFRACTION100
1.3768-1.42120.2361440.22151282X-RAY DIFFRACTION100
1.4212-1.4720.26481400.2121265X-RAY DIFFRACTION100
1.472-1.53090.25031420.18481292X-RAY DIFFRACTION100
1.5309-1.60060.221480.19351295X-RAY DIFFRACTION100
1.6006-1.68490.24611440.20191259X-RAY DIFFRACTION100
1.6849-1.79040.26261460.20081274X-RAY DIFFRACTION100
1.7904-1.92860.23311380.18741272X-RAY DIFFRACTION100
1.9286-2.12250.20061480.16311262X-RAY DIFFRACTION100
2.1225-2.42920.21641440.1691283X-RAY DIFFRACTION100
2.4292-3.05880.18961580.19351271X-RAY DIFFRACTION100
3.0588-20.350.23461310.19631098X-RAY DIFFRACTION86

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