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- PDB-5ejj: Crystal structure of UfSP from C.elegans -

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Basic information

Entry
Database: PDB / ID: 5ejj
TitleCrystal structure of UfSP from C.elegans
ComponentsUfm1-specific protease
KeywordsHYDROLASE / Ufm1 / UfSP / Deufmylation
Function / homology
Function and homology information


protein localization to non-motile cilium / UFM1 hydrolase activity / positive regulation of chemotaxis / chemotaxis / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / response to ethanol / proteolysis / endoplasmic reticulum membrane / perinuclear region of cytoplasm / protein-containing complex
Similarity search - Function
Peptidase C78, ubiquitin fold modifier-specific peptidase 1/ 2 / Peptidase family C78 / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ufm1-specific protease
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKim, K. / Ha, B. / Kim, E.E.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future PlanningNRF 20110021713 Korea, Republic Of
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2016
Title: The MPN domain of Caenorhabditis elegans UfSP modulates both substrate recognition and deufmylation activity
Authors: Ha, B.H. / Kim, K.H. / Yoo, H.M. / Lee, W. / Kim, E.E.
History
DepositionNov 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ufm1-specific protease
B: Ufm1-specific protease


Theoretical massNumber of molelcules
Total (without water)128,1902
Polymers128,1902
Non-polymers00
Water4,017223
1
A: Ufm1-specific protease


Theoretical massNumber of molelcules
Total (without water)64,0951
Polymers64,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ufm1-specific protease


Theoretical massNumber of molelcules
Total (without water)64,0951
Polymers64,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ufm1-specific protease

B: Ufm1-specific protease


Theoretical massNumber of molelcules
Total (without water)128,1902
Polymers128,1902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_764-x+5/2,-y+1,z-1/21
Buried area1440 Å2
ΔGint-13 kcal/mol
Surface area47520 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)77.531, 149.808, 226.420
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 Ufm1-specific protease / UfSP / Odorant response abnormal protein 8


Mass: 64095.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: odr-8, ufsp-2, F38A5.1 / Plasmid: pET28a / Cell line (production host): BL21RIL / Production host: Escherichia coli (E. coli)
References: UniProt: Q94218, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.13 Å3/Da / Density % sol: 76.02 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Bicine, Ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 66417 / % possible obs: 93.8 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 28.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 1.65 / % possible all: 77.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data processing
SOLVEphasing
RESOLVEphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→41.278 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 3723 3.21 %
Rwork0.2056 --
obs0.2066 62217 91.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→41.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8307 0 0 223 8530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018502
X-RAY DIFFRACTIONf_angle_d1.30111517
X-RAY DIFFRACTIONf_dihedral_angle_d16.8553095
X-RAY DIFFRACTIONf_chiral_restr0.0931257
X-RAY DIFFRACTIONf_plane_restr0.0051485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7924-2.82770.3489850.34542621X-RAY DIFFRACTION58
2.8277-2.86490.33951130.32333332X-RAY DIFFRACTION73
2.8649-2.90420.34441140.30283554X-RAY DIFFRACTION79
2.9042-2.94560.37131230.30483672X-RAY DIFFRACTION80
2.9456-2.98960.33671240.30273708X-RAY DIFFRACTION82
2.9896-3.03630.35851240.28393809X-RAY DIFFRACTION85
3.0363-3.08610.2771280.27153871X-RAY DIFFRACTION85
3.0861-3.13930.29941310.27133931X-RAY DIFFRACTION87
3.1393-3.19630.31231380.26614028X-RAY DIFFRACTION88
3.1963-3.25780.29751360.24364037X-RAY DIFFRACTION89
3.2578-3.32430.30581380.24054181X-RAY DIFFRACTION92
3.3243-3.39650.26781410.22174253X-RAY DIFFRACTION93
3.3965-3.47550.27471380.22044266X-RAY DIFFRACTION94
3.4755-3.56230.24531410.21594336X-RAY DIFFRACTION96
3.5623-3.65860.20751500.19614416X-RAY DIFFRACTION97
3.6586-3.76620.20591450.19344436X-RAY DIFFRACTION98
3.7662-3.88770.24651480.18254450X-RAY DIFFRACTION98
3.8877-4.02650.21311520.17984497X-RAY DIFFRACTION99
4.0265-4.18760.24081470.17784485X-RAY DIFFRACTION99
4.1876-4.37790.19231500.17084532X-RAY DIFFRACTION100
4.3779-4.60850.18771520.16514530X-RAY DIFFRACTION100
4.6085-4.89680.21681530.16314544X-RAY DIFFRACTION100
4.8968-5.27420.21731500.1684506X-RAY DIFFRACTION100
5.2742-5.80360.25291470.19144539X-RAY DIFFRACTION100
5.8036-6.64040.23421520.21134515X-RAY DIFFRACTION100
6.6404-8.35480.20161530.21384551X-RAY DIFFRACTION100
8.3548-41.28270.22351500.21474502X-RAY DIFFRACTION99

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