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- PDB-3tb3: Crystal structure of the UCH domain of UCH-L5 with 6 residues deleted -

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Basic information

Entry
Database: PDB / ID: 3tb3
TitleCrystal structure of the UCH domain of UCH-L5 with 6 residues deleted
ComponentsUbiquitin carboxyl-terminal hydrolase isozyme L5
KeywordsHYDROLASE / UCH domain
Function / homology
Function and homology information


lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / positive regulation of smoothened signaling pathway / midbrain development / regulation of chromosome organization / endopeptidase inhibitor activity ...lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / positive regulation of smoothened signaling pathway / midbrain development / regulation of chromosome organization / endopeptidase inhibitor activity / proteasome binding / protein deubiquitination / regulation of DNA replication / regulation of embryonic development / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of DNA repair / regulation of proteasomal protein catabolic process / positive regulation of DNA repair / telomere maintenance / Downregulation of TGF-beta receptor signaling / UCH proteinases / ubiquitin-dependent protein catabolic process / DNA recombination / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / regulation of cell cycle / chromatin remodeling / DNA repair / nucleolus / positive regulation of DNA-templated transcription / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily ...Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase isozyme L5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZhou, Z.R. / Zha, M. / Zhou, J. / Hu, H.Y.
CitationJournal: Biochem.J. / Year: 2012
Title: Length of the active-site crossover loop defines the substrate specificity of ubiquitin C-terminal hydrolases for ubiquitin chains.
Authors: Zhou, Z.R. / Zhang, Y.H. / Liu, S. / Song, A.X. / Hu, H.Y.
History
DepositionAug 5, 2011Deposition site: RCSB / Processing site: PDBJ
SupersessionFeb 22, 2012ID: 3SQA
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
B: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4464
Polymers51,3662
Non-polymers802
Water77543
1
A: Ubiquitin carboxyl-terminal hydrolase isozyme L5


Theoretical massNumber of molelcules
Total (without water)25,6831
Polymers25,6831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7633
Polymers25,6831
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.540, 102.340, 47.060
Angle α, β, γ (deg.)90.000, 92.130, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUARGARGchain A and (resseq 7:145 or resseq 162:226 )AA7 - 1459 - 147
12ALAALAASPASPchain A and (resseq 7:145 or resseq 162:226 )AA162 - 226164 - 228
21GLUGLUARGARGchain B and (resseq 7:145 or resseq 162:226 )BB7 - 1459 - 147
22ALAALAASPASPchain B and (resseq 7:145 or resseq 162:226 )BB162 - 226164 - 228

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L5 / UCH-L5 / Ubiquitin C-terminal hydrolase UCH37 / Ubiquitin thioesterase L5


Mass: 25682.881 Da / Num. of mol.: 2 / Fragment: UCH domain (UNP RESIDUES 1-227) / Mutation: C88A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AD-019, CGI-70, UCH-L5, UCH37, UCHL5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5K5, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Calcium Acetate hydrate, 0.1M Sodium Cacodylate, 18% w/v PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorDetector: CCD / Date: Apr 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 19479 / Num. obs: 19479 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rsym value: 0.07
Reflection shellResolution: 2.3→2.38 Å / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A7S

3a7s


Resolution: 2.3→32.318 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7985 / SU ML: 0.87 / σ(F): 1.37 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.269 615 3.17 %RANDOM
Rwork0.2219 ---
obs0.2234 19377 96.69 %-
all-19479 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.807 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 191.01 Å2 / Biso mean: 76.0153 Å2 / Biso min: 26.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.1378 Å20 Å2-2.229 Å2
2---2.0019 Å2-0 Å2
3---2.1398 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 2 43 3275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083302
X-RAY DIFFRACTIONf_angle_d1.0444468
X-RAY DIFFRACTIONf_chiral_restr0.08486
X-RAY DIFFRACTIONf_plane_restr0.004586
X-RAY DIFFRACTIONf_dihedral_angle_d15.0911196
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1615X-RAY DIFFRACTIONPOSITIONAL0.046
12B1615X-RAY DIFFRACTIONPOSITIONAL0.046
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.53140.34471630.31784780494399
2.5314-2.89750.33911590.263848224981100
2.8975-3.64970.29061410.23064721486297
3.6497-32.3210.23491520.19524439459191
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)
14.0107-1.7305-1.48643.89131.64464.83360.2598-0.1505-0.41940.06750.0553-0.31650.0605-0.2137-0.140.26380.0409-0.01640.248-0.05010.3018.394115.94220.749
28.0825-4.2856-1.69537.0293-0.4496.284-0.6544-0.3094-0.79231.44580.45051.8068-0.2128-0.47620.01830.4574-0.02370.15040.4408-0.03980.54131.240134.1787-1.2354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 7:145) or (chain A and resid 162:226)A7 - 145
2X-RAY DIFFRACTION1(chain A and resid 7:145) or (chain A and resid 162:226)A162 - 226
3X-RAY DIFFRACTION2(chain B and resid 7:145) or (chain B and resid 162:226)B7 - 145
4X-RAY DIFFRACTION2(chain B and resid 7:145) or (chain B and resid 162:226)B162 - 226

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