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- PDB-6sjh: Structure of the PRY-SPRY domain of human Trim16L/Trim70 -

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Basic information

Entry
Database: PDB / ID: 6sjh
TitleStructure of the PRY-SPRY domain of human Trim16L/Trim70
ComponentsTripartite motif-containing protein 16-like protein
KeywordsUNKNOWN FUNCTION / Unknown
Function / homology
Function and homology information


plasma membrane / cytosol
Similarity search - Function
SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Tripartite motif-containing protein 16-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMikkelsen, J.H. / Andersen, C.B.F.
CitationJournal: To Be Published
Title: Structure of the PRY-SPRY domain of human Trim16L/Trim70
Authors: Mikkelsen, J.H. / Andersen, C.B.F.
History
DepositionAug 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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: Tripartite motif-containing protein 16-like protein
B: Tripartite motif-containing protein 16-like protein
C: Tripartite motif-containing protein 16-like protein


Theoretical massNumber of molelcules
Total (without water)66,9453
Polymers66,9453
Non-polymers00
Water11,476637
1
A: Tripartite motif-containing protein 16-like protein


Theoretical massNumber of molelcules
Total (without water)22,3151
Polymers22,3151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tripartite motif-containing protein 16-like protein


Theoretical massNumber of molelcules
Total (without water)22,3151
Polymers22,3151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tripartite motif-containing protein 16-like protein


Theoretical massNumber of molelcules
Total (without water)22,3151
Polymers22,3151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.780, 95.770, 116.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Tripartite motif-containing protein 16-like protein / Tripartite motif-containing protein 70


Mass: 22315.129 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM16L, TRIM70 / Production host: Escherichia coli (E. coli) / References: UniProt: Q309B1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: Na-acetate, PEG 400, PGA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 221803 / % possible obs: 88.3 % / Redundancy: 2.48 % / CC1/2: 0.993 / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.04
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 2.34 % / Num. unique obs: 95480 / CC1/2: 0.644 / Rrim(I) all: 0.555 / % possible all: 92.1

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B8E

4b8e


Resolution: 1.5→30 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2117 2000 0.82 %
Rwork0.1809 --
obs0.1821 221803 88.3 %
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4679 0 0 637 5316

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