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- PDB-1vjv: Crystal structure of Ubiquitin carboxyl-terminal hydrolase 6 (yfr... -

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Basic information

Entry
Database: PDB / ID: 1vjv
TitleCrystal structure of Ubiquitin carboxyl-terminal hydrolase 6 (yfr010w) from Saccharomyces cerevisiae at 1.74 A resolution
ComponentsUbiquitin carboxyl-terminal hydrolase 6
KeywordsHYDROLASE / yfr010w / UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 6 / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


mitochondria-associated ubiquitin-dependent protein catabolic process / negative regulation of proteasomal protein catabolic process / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome regulatory particle / Ub-specific processing proteases / proteasome binding / protein deubiquitination / regulation of proteasomal protein catabolic process / proteasome complex / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity
Similarity search - Function
Helix Hairpins - #1140 / Ubiquitin carboxyl-terminal hydrolase 14-like / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases ...Helix Hairpins - #1140 / Ubiquitin carboxyl-terminal hydrolase 14-like / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases / Helix Hairpins / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Helix non-globular / Special / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.74 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Ubiquitin carboxyl-terminal hydrolase 6 (yfr010w) from Saccharomyces cerevisiae at 1.74 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999SEQUENCE MASS SPECTROMETER DATA AND SEQUENCING THE CONSTRUCT CONFIRMED THAT THE EXPRESSED PROTEIN ...SEQUENCE MASS SPECTROMETER DATA AND SEQUENCING THE CONSTRUCT CONFIRMED THAT THE EXPRESSED PROTEIN COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] FOLLOWED BY RESIDUES 97-499 OF THE PREDICTED YFR010W GENE PRODUCT. CLONING ARTIFACT: THE DENSITY FOR RESIDUE 182 FROM EACH MONOMER SUGGESTED THAT THIS RESIDUE WAS AN VALINE AND NOT AN ISOLUCINE. SEQUENCING OF THE CONSTRUCT CONFIRMED THAT RESIDUE 182 IS VALINE IN THE EXPRESSED PROTEIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 6


Theoretical massNumber of molelcules
Total (without water)48,6471
Polymers48,6471
Non-polymers00
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.231, 79.449, 106.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 6 / Ubiquitin thiolesterase 6 / Ubiquitin-specific processing protease 6 / Deubiquitinating enzyme 6


Mass: 48647.398 Da / Num. of mol.: 1 / Fragment: residues 97-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBP6, YFR010W / Production host: Escherichia coli (E. coli) / References: UniProt: P43593, EC: 3.1.2.15
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1442.44
22.2945.77
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2771vapor diffusion, sitting drop, nanodrop16% PEG MME 2000, 0.03M Tris_base, 0.07M Tris Cl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop21% PEG MME 2000, 0.03M Tris_base, 0.07M Tris Cl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.3.111.11587
SYNCHROTRONAPS 19-BM20.96112, 0.97963,0.97946
Detector
TypeIDDetectorDateDetails
ADSC1CCDJul 25, 2003
APS 2CCDJul 17, 2003water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Rosenbaum-Rock double-crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
20.961121
30.979631
40.979461
ReflectionResolution: 1.74→79.45 Å / Num. obs: 42823 / % possible obs: 98.2 % / Redundancy: 4 % / Biso Wilson estimate: 36.27 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.3
Reflection shellResolution: 1.74→1.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2820 / % possible all: 89.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SHELXDphasing
autoSHARPphasing
SOLOMONphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.74→63.65 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.624 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20892 2129 5 %RANDOM
Rwork0.17917 ---
obs0.18069 40625 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.059 Å2
Baniso -1Baniso -2Baniso -3
1--2.92 Å20 Å20 Å2
2--0.32 Å20 Å2
3---2.59 Å2
Refinement stepCycle: LAST / Resolution: 1.74→63.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 0 241 3205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223063
X-RAY DIFFRACTIONr_bond_other_d0.0020.022725
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9544119
X-RAY DIFFRACTIONr_angle_other_deg0.76736395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665362
X-RAY DIFFRACTIONr_chiral_restr0.0860.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023349
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02601
X-RAY DIFFRACTIONr_nbd_refined0.2010.2545
X-RAY DIFFRACTIONr_nbd_other0.2380.23127
X-RAY DIFFRACTIONr_nbtor_other0.0840.21783
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2189
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.27
X-RAY DIFFRACTIONr_mcbond_it1.88931833
X-RAY DIFFRACTIONr_mcangle_it3.12652964
X-RAY DIFFRACTIONr_scbond_it5.01881230
X-RAY DIFFRACTIONr_scangle_it7.49111155
LS refinement shellResolution: 1.74→1.817 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.324 220 4.62 %
Rwork0.272 4544 -
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)
11.73870.2808-0.26981.0312-0.24910.76520.0581-0.0019-0.03540.0596-0.038-0.1391-0.0327-0.0134-0.02020.1090.0017-0.00410.0797-0.02040.04316.88521.71322.76
20.7899-2.1909-0.34445.92512.98287.97640.07450.0468-0.27490.0359-0.18470.22740.6963-0.56210.11020.1445-0.12360.03660.179-0.00050.1069-13.2957.3623.481
39.2697-3.0023-9.89792.58565.920215.39880.05110.18740.0579-0.1187-0.1216-0.01410.0123-0.1110.07050.14430.0685-0.05170.1409-0.00870.0564-4.6625.9781.406
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11103 - 34319 - 259
21418 - 499334 - 415
32344 - 370260 - 286
43387 - 417303 - 333

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