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- PDB-6yjk: Structure of CYRI-B (FAM49B) from Rhincodon typus -

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Basic information

Entry
Database: PDB / ID: 6yjk
TitleStructure of CYRI-B (FAM49B) from Rhincodon typus
ComponentsCYRI-B (FAM49B)
KeywordsCYTOSOLIC PROTEIN / CYRI-B / FAM49B / actin assembly / Rac binding protein / cell motility regulator
Biological speciesRhincodon typus (whale shark)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.37 Å
AuthorsKaplan, E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N000994/1 United Kingdom
Wellcome Trust101828/Z/13/Z United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structure of CYRI-B (FAM49B), a key regulator of cellular actin assembly.
Authors: Kaplan, E. / Stone, R. / Hume, P.J. / Greene, N.P. / Koronakis, V.
History
DepositionApr 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYRI-B (FAM49B)


Theoretical massNumber of molelcules
Total (without water)36,9101
Polymers36,9101
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.810, 72.230, 107.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYRI-B (FAM49B)


Mass: 36909.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhincodon typus (whale shark) / Gene: fam49b / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) glycerol ethoxylate, 0.2 M ammonium acetate and 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.37→60.01 Å / Num. obs: 13266 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.041 / Rrim(I) all: 0.134 / Net I/σ(I): 10.1 / Num. measured all: 138576 / Scaling rejects: 538
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.37-2.467.51.031021413620.590.3961.1072100
8.87-60.018.20.04525613130.9980.0160.04828.599.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.53 Å60.01 Å

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.25data extraction
PHENIX1.14_3260refinement
REFMAC7.0.078refinement
PHASER2.8.2phasing
Aimless0.7.3data scaling
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YJJ

6yjj


Resolution: 2.37→60.007 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 661 5 %RANDOM
Rwork0.2251 12546 --
obs0.2276 13207 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.09 Å2 / Biso mean: 74.5724 Å2 / Biso min: 31.37 Å2
Refinement stepCycle: final / Resolution: 2.37→60.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 0 8 2564
Biso mean---45.53 -
Num. residues----320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3701-2.55310.36851110.36752471
2.5531-2.81010.321490.28922436
2.8101-3.21670.32021360.25972480
3.2167-4.05250.27611450.21572503
4.0525-600.23281200.18582656
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.89940.1132.45343.14761.68648.4845-0.1505-0.42130.24120.4137-0.01670.0131-0.2328-0.78180.140.53350.01330.03230.31460.00240.37553.68314.0076-26.2348
23.0076-0.21741.56872.4712-1.07435.7652-0.08690.0548-0.072-0.2096-0.0418-0.07850.89660.22360.11490.6805-0.0250.0330.264-0.01980.359613.32644.1536-20.9671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 164 )A0 - 164
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 324 )A165 - 324

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