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- PDB-6yjj: Structure of CYRI-B (FAM49B) from Rhincodon typus (selenomethioni... -

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Basic information

Entry
Database: PDB / ID: 6yjj
TitleStructure of CYRI-B (FAM49B) from Rhincodon typus (selenomethionine derivative)
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 / SAD / Resolution: 2.4 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 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)37,3791
Polymers37,3791
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 area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.400, 72.820, 107.320
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: 37378.848 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
Has ligand of interestN
Has protein modificationY

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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: 42.31 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.1 M Bis-Tris pH 5.5 and 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9611 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 2.4→72.82 Å / Num. obs: 13006 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.042 / Rrim(I) all: 0.13 / Net I/σ(I): 12.8 / Num. measured all: 123774 / Scaling rejects: 39
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
2.4-2.498.21.0321088913290.7820.3821.1022.1100
8.98-72.828.10.05224853080.9970.0180.05536.799.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.25data extraction
PHENIX1.14_3260refinement
REFMAC7.0.078refinement
PHASERphasing
Aimless0.7.3data scaling
iMOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.4→53.66 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 638 4.92 %RANDOM
Rwork0.2048 12321 --
obs0.2067 12959 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.31 Å2 / Biso mean: 63.28 Å2 / Biso min: 23.68 Å2
Refinement stepCycle: final / Resolution: 2.4→53.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 0 8 2564
Biso mean---42.51 -
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
2.4-2.58530.32821200.28142405
2.5853-2.84550.33411260.25432410
2.8455-3.25720.2831390.23272425
3.2572-4.10350.23561260.19782483
4.1035-53.660.19551270.17582598
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)
11.32710.13651.64342.14281.46225.8316-0.0797-0.31920.29580.3059-0.0893-0.0207-0.0831-0.5490.14960.3650.00090.00490.2776-0.0280.41073.698813.9862-26.043
22.1457-0.23081.57982.4619-0.82475.28160.0597-0.0313-0.0055-0.1137-0.1071-0.01260.82540.20310.02780.4656-0.00140.02630.2858-0.02940.442613.39084.2093-20.8678
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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