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- PDB-3ebq: Crystal structure of human PPPDE1 -

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Basic information

Entry
Database: PDB / ID: 3ebq
TitleCrystal structure of human PPPDE1
ComponentsMOLECULE: PPPDE1 (PERMUTED PAPAIN FOLD PEPTIDASES OF DSRNA VIRUSES AND EUKARYOTES 1), UPF0326 protein FAM152B
KeywordsHYDROLASE / PEPTIDASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / THIOL PROTEASE / UBL CONJUGATION PATHWAY
Function / homology
Function and homology information


protein modification by small protein removal / palmitoyl-(protein) hydrolase activity / palmitoyl[protein] hydrolase / long-chain fatty acyl-CoA hydrolase activity / deSUMOylase activity / protein desumoylation / regulation of proteasomal ubiquitin-dependent protein catabolic process / importin-alpha family protein binding / Hydrolases; Acting on peptide bonds (peptidases) / protein export from nucleus ...protein modification by small protein removal / palmitoyl-(protein) hydrolase activity / palmitoyl[protein] hydrolase / long-chain fatty acyl-CoA hydrolase activity / deSUMOylase activity / protein desumoylation / regulation of proteasomal ubiquitin-dependent protein catabolic process / importin-alpha family protein binding / Hydrolases; Acting on peptide bonds (peptidases) / protein export from nucleus / protein-containing complex / proteolysis / identical protein binding / nucleus / cytosol
Similarity search - Function
PPPDE domains / PPPDE peptidase domain superfamily / PPPDE putative peptidase domain / PPPDE putative peptidase domain / PPPDE peptidase domain / PPPDE domain profile. / endopeptidase fold (from Nostoc punctiforme) / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Desumoylating isopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.9 Å
AuthorsWalker, J.R. / Akutsu, M. / Qiu, L. / Li, Y. / Slessarev, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. ...Walker, J.R. / Akutsu, M. / Qiu, L. / Li, Y. / Slessarev, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of Human PPPDE1
Authors: Walker, J.R. / Akutsu, M. / Qiu, L. / Li, Y. / Slessarev, Y. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionAug 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: MOLECULE: PPPDE1 (PERMUTED PAPAIN FOLD PEPTIDASES OF DSRNA VIRUSES AND EUKARYOTES 1), UPF0326 protein FAM152B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8223
Polymers18,4211
Non-polymers4012
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.625, 41.625, 184.239
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein MOLECULE: PPPDE1 (PERMUTED PAPAIN FOLD PEPTIDASES OF DSRNA VIRUSES AND EUKARYOTES 1), UPF0326 protein FAM152B


Mass: 18420.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM152B / Plasmid: PET28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-V2R
References: UniProt: Q6ICB0, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.17 Å3/Da / Density % sol: 43.22 % / Description: MERCURY DERIVATIVE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 10% PEG 4000, 0.1 M SODIUM, ACETATE, 0.1 M TRIS HCL PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K. CRYSTALS WERE SOAKED OVERNIGHT IN 0.01 M THIMEROSAL TO CREATE THE MERCURY DERIVATIVE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 10, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 13493 / Num. obs: 13493 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Rsym value: 0.068 / Net I/σ(I): 45.21
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.57 / Num. unique all: 1162 / Rsym value: 0.646 / % possible all: 87.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SOLVEphasing
RESOLVEmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→28.04 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.625 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUMOF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27273 670 5 %RANDOM
Rwork0.22354 ---
obs0.22585 12727 98.19 %-
all-13493 --
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: 38.566 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 3 63 1190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221155
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9851576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3235147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96924.37548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82515180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.889154
X-RAY DIFFRACTIONr_chiral_restr0.1030.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02887
X-RAY DIFFRACTIONr_nbd_refined0.2180.2518
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.24
X-RAY DIFFRACTIONr_mcbond_it1.0121.5746
X-RAY DIFFRACTIONr_mcangle_it1.50521178
X-RAY DIFFRACTIONr_scbond_it2.4393463
X-RAY DIFFRACTIONr_scangle_it3.5244.5398
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 46 -
Rwork0.254 770 -
obs--85.27 %
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)
11.89471.03821.84352.63521.34362.29490.08610.0550.08710.27860.20060.3448-0.1588-0.0602-0.28670.05010.01170.0141-0.00670.04460.0825.934823.922874.4846
220.3053-7.8928-12.046626.51293.08617.2556-0.3741-1.26881.92820.12691.2173-0.0706-0.70581.2899-0.84320.07050.0504-0.12650.1086-0.12620.074323.035129.938785.9019
326.30483.202412.49626.3756-7.203318.6530.2872-0.0306-0.7117-0.3030.1164-0.49790.2304-0.283-0.4036-0.05830.132-0.07630.0339-0.1150.105328.341625.001284.2223
42.1221.62152.24872.81610.29373.6695-0.05730.2387-0.13910.45980.22430.3363-0.22330.0837-0.1670.0540.05210.0285-0.0020.0180.06535.133720.314776.1654
55.364-7.32950.832316.3524-2.62461.81140.2334-0.43970.12550.69780.22460.25190.0047-0.1944-0.4580.08810.04560.12260.02750.01020.0051.167614.25280.9382
63.31820.61281.21683.47680.57082.0195-0.2518-0.17270.24460.40180.19370.4717-0.4923-0.04740.05810.13520.09490.095-0.022-0.00670.03195.207725.704777.7944
76.72288.542-8.1421.7011-10.0169.8657-0.38780.46380.357-0.45850.41140.9150.1312-0.2856-0.0236-0.0404-0.04-0.13310.01510.08450.1674-4.010713.870364.4783
85.3334-3.08191.1473.7771-0.60463.08850.0003-0.0545-0.01110.3691-0.03750.3647-0.0784-0.14650.03730.0285-0.02410.0213-0.0090.03360.12610.54414.645672.3535
99.63672.66432.95010.91072.640220.02690.0544-0.261-0.61240.20460.007-0.26830.4929-0.5087-0.06140.11120.01820.0142-0.03930.05190.08267.04072.92680.2089
101.16940.62621.82231.9608-0.93635.0890.06810.075-0.06350.10880.1034-0.0230.04030.114-0.17160.06230.0364-0.0160.0102-0.01330.064512.005511.331375.6696
111.68771.61461.23023.04180.6542.7084-0.0340.08890.1304-0.15820.1158-0.11090.10030.0997-0.08180.042-0.0024-0.00040.01910.00020.05412.73617.576867.7251
1248.3659-0.407138.1662.9292-6.862444.74160.4768-1.15020.0473-0.7116-0.6942-0.02880.1175-0.5030.2175-0.02990.0412-0.00650.0087-0.04720.058524.005816.022479.7725
1316.89773.11468.768212.0185-6.73137.899-0.6033-0.2784-0.26-0.0620.609-0.6827-0.03610.0669-0.0056-0.04660.0685-0.0250.1455-0.0012-0.035829.267315.081886.2384
142.74440.9405-7.44061.8051-9.991757.5202-0.2792-1.8648-0.3102-1.3119-0.082-1.58592.6264-2.80160.36130.1827-0.1682-0.08430.1969-0.0309-0.104123.37269.820990.7349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 2024 - 39
2X-RAY DIFFRACTION2AA21 - 2540 - 44
3X-RAY DIFFRACTION3AA26 - 3345 - 52
4X-RAY DIFFRACTION4AA34 - 4953 - 68
5X-RAY DIFFRACTION5AA50 - 6169 - 80
6X-RAY DIFFRACTION6AA62 - 7481 - 93
7X-RAY DIFFRACTION7AA75 - 8494 - 103
8X-RAY DIFFRACTION8AA85 - 95104 - 114
9X-RAY DIFFRACTION9AA96 - 100115 - 119
10X-RAY DIFFRACTION10AA101 - 117120 - 136
11X-RAY DIFFRACTION11AA118 - 130137 - 149
12X-RAY DIFFRACTION12AA131 - 136150 - 155
13X-RAY DIFFRACTION13AA137 - 142156 - 161
14X-RAY DIFFRACTION14AA143 - 148162 - 167

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