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- PDB-6drm: OTU domain of Fam105A -

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Basic information

Entry
Database: PDB / ID: 6drm
TitleOTU domain of Fam105A
ComponentsInactive ubiquitin thioesterase FAM105A
KeywordsHYDROLASE / Fam105A / OTUpseu / deubiquitinase / OTU domain / pseudo-enzyme
Function / homologyInactive ubiquitin thioesterase OTULINL / FAM105 / Peptidase family C101 / cytoplasmic side of endoplasmic reticulum membrane / nuclear envelope / cytoplasm / Inactive ubiquitin thioesterase OTULINL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å
AuthorsCeccarelli, D.F. / Sicheri, F. / Cordes, S.
CitationJournal: Structure / Year: 2019
Title: FAM105A/OTULINL Is a Pseudodeubiquitinase of the OTU-Class that Localizes to the ER Membrane.
Authors: Ceccarelli, D.F. / Ivantsiv, S. / Mullin, A.A. / Coyaud, E. / Manczyk, N. / Maisonneuve, P. / Kurinov, I. / Zhao, L. / Go, C. / Gingras, A.C. / Raught, B. / Cordes, S. / Sicheri, F.
History
DepositionJun 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.page_first ..._citation.journal_id_CSD / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inactive ubiquitin thioesterase FAM105A


Theoretical massNumber of molelcules
Total (without water)32,7321
Polymers32,7321
Non-polymers00
Water66737
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 area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.170, 53.870, 41.520
Angle α, β, γ (deg.)90.000, 101.940, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Inactive ubiquitin thioesterase FAM105A


Mass: 32731.766 Da / Num. of mol.: 1 / Fragment: OTU domain residues 87-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM105A / Plasmid: ProEx / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NUU6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 6% PEG8000, 0.1M Tris-HCl pH 8.0, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.06→39.906 Å / Num. obs: 22648 / % possible obs: 98.8 % / Redundancy: 3.709 % / Biso Wilson estimate: 47.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.046 / Χ2: 1.021 / Net I/σ(I): 17.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.06-2.113.5211.0321.1415840.6381.21796.5
2.11-2.173.7730.7231.7316100.7970.84297.4
2.17-2.233.7810.542.3415680.8770.62998.8
2.23-2.33.7550.3953.3415490.930.46298.7
2.3-2.383.7850.3084.1614610.9490.35998.8
2.38-2.463.7740.2275.4614770.970.26599.3
2.46-2.563.7850.1767.3613830.9810.20598.8
2.56-2.663.7690.1319.4313350.9890.15399.3
2.66-2.783.7640.09912.4813030.9930.11699.4
2.78-2.913.7620.07515.8812260.9960.08899.4
2.91-3.073.7570.05320.9911700.9980.06199.1
3.07-3.263.7250.0426.4811190.9980.04798.9
3.26-3.483.6910.03233.0710610.9990.03898.9
3.48-3.763.6750.02641.049760.9990.0399.6
3.76-4.123.5840.02343.379080.9990.02799.3
4.12-4.613.5550.02248.678210.9990.02699.6
4.61-5.323.5710.02348.787300.9990.02799.3
5.32-6.513.6450.0248.146090.9990.02499.5
6.51-9.213.6270.01752.354880.9990.0299.4
9.21-39.9063.2370.02552.262700.9970.03194.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
XDS20170923data reduction
XSCALE20170923data scaling
PHASER2.5.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KSJ

4ksj


Resolution: 2.06→39.906 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.2
RfactorNum. reflection% reflection
Rfree0.2272 1110 4.9 %
Rwork0.2064 --
obs0.2075 22642 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 160.54 Å2 / Biso mean: 68.6007 Å2 / Biso min: 34.8 Å2
Refinement stepCycle: final / Resolution: 2.06→39.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 0 37 2270
Biso mean---54.83 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.06-2.15380.36631310.33652596272797
2.1538-2.26730.29141490.28642650279999
2.2673-2.40930.28621310.24992679281099
2.4093-2.59530.26841250.24422710283599
2.5953-2.85640.24461250.23882711283699
2.8564-3.26960.26451310.24212699283099
3.2696-4.11870.24241590.20112724288399
4.1187-39.91310.17691590.16092763292299
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)
18.36060.74930.62854.2462-0.89684.8829-0.0126-0.87150.50390.38310.09030.6074-0.6545-0.4593-0.06710.56960.00560.10120.5708-0.01810.47-47.046-3.549811.2642
26.65092.1222-0.10143.5857-0.46022.67550.069-0.4149-0.10880.1622-0.0706-0.4249-0.0650.67740.0210.32650.0553-0.0610.5392-0.04190.3072-17.5091-2.80353.2753
32.50670.1479-0.29552.104-1.61164.08380.0897-0.342-0.0106-0.05220.0148-0.06060.01690.3722-0.10970.3522-0.03390.0050.5037-0.13580.3997-21.77172.2945-1.3281
46.9511-1.0191-3.224.07-1.81323.79560.12250.53810.1389-0.12720.30310.275-0.1051-0.4088-0.24510.417-0.0619-0.02680.5153-0.04260.5161-37.9321-1.8048-1.3408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 87 through 125 )A87 - 125
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 214 )A126 - 214
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 309 )A215 - 309
4X-RAY DIFFRACTION4chain 'A' and (resid 310 through 356 )A310 - 356

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