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- PDB-7qs5: Crystal structure of B30.2 PRYSPRY domain of TRIM67 -

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Basic information

Entry
Database: PDB / ID: 7qs5
TitleCrystal structure of B30.2 PRYSPRY domain of TRIM67
ComponentsTripartite motif-containing protein 67
KeywordsLIGASE / E3 / TRIM / TRIM67 / B30.2 domain / SPRY domain / PRYSPRY domain
Function / homology
Function and homology information


positive regulation of ubiquitin-dependent protein catabolic process / negative regulation of Ras protein signal transduction / positive regulation of neuron projection development / regulation of protein localization / cytoskeleton / zinc ion binding / cytoplasm
Similarity search - Function
COS domain / COS domain profile. / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) ...COS domain / COS domain profile. / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / 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. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like fold
Similarity search - Domain/homology
Tripartite motif-containing protein 67
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsChaikuad, A. / Zhubi, R. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of B30.2 PRYSPRY domain of TRIM67
Authors: Chaikuad, A. / Zhubi, R. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionJan 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tripartite motif-containing protein 67
B: Tripartite motif-containing protein 67
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,08021
Polymers39,9012
Non-polymers1,17919
Water3,981221
1
A: Tripartite motif-containing protein 67
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,69513
Polymers19,9501
Non-polymers74512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tripartite motif-containing protein 67
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3858
Polymers19,9501
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.392, 135.392, 35.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0 / Auth seq-ID: 609 - 766 / Label seq-ID: 6 - 163

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Tripartite motif-containing protein 67 / TRIM9-like protein


Mass: 19950.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM67, TNL / Plasmid: pGTVL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 / References: UniProt: Q6ZTA4
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20% high molecular weight PEG Smears, 0.1M acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99981 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99981 Å / Relative weight: 1
ReflectionResolution: 1.65→47.87 Å / Num. obs: 39503 / % possible obs: 99.9 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.021 / Rrim(I) all: 0.069 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.6910.80.9472.429170.8510.3191.05100
7.38-47.8710.10.0564890.9940.0190.05999.6

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B2S

7b2s


Resolution: 1.65→47.87 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.463 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0867 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1771 1884 4.8 %RANDOM
Rwork0.1548 ---
obs0.1559 37611 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.17 Å2 / Biso mean: 28.266 Å2 / Biso min: 15.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.05 Å2
Refinement stepCycle: final / Resolution: 1.65→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 80 221 2868
Biso mean--47.53 39.51 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132734
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152482
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.6473691
X-RAY DIFFRACTIONr_angle_other_deg1.4611.5845691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8745339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.28722.8150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25615407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6131514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023131
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02665
Refine LS restraints NCS

Ens-ID: 1 / Number: 5257 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 142 -
Rwork0.235 2769 -
all-2911 -
obs--100 %
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)
12.36270.87110.46382.29590.16121.42360.01870.15770.0076-0.16980.0010.1722-0.1262-0.0036-0.01970.02970.0122-0.01380.0193-0.0060.015647.776710.9767-10.4737
23.122-0.0177-0.35742.796-0.25861.1799-0.04890.06510.10370.0097-0.0605-0.3413-0.02240.2150.10950.01610.0043-0.02110.05280.0150.0777.112322.057-4.713
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A609 - 772
2X-RAY DIFFRACTION2B605 - 768

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