[English] 日本語
Yorodumi
- PDB-5nkz: Crystal structure of H. polymorpha ubiquitin conjugating enzyme P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nkz
TitleCrystal structure of H. polymorpha ubiquitin conjugating enzyme Pex4p in complex with soluble domain of Pex22p
Components
  • Peroxin 22
  • Ubiquitin-conjugating enzyme E2-21 kDa
KeywordsTRANSFERASE / Pex4 / Pex22 / Ubiquitin conjugating enzyme / Crystallization / Hansenula polymorpha / Peroxisome import
Function / homology
Function and homology information


peroxisome organization / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin-protein transferase activity / membrane => GO:0016020 / protein ubiquitination / ATP binding
Similarity search - Function
Peroxisome assembly protein 22 / Peroxin 22, C-terminal domain superfamiliy / Peroxisomal biogenesis protein family / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme ...Peroxisome assembly protein 22 / Peroxin 22, C-terminal domain superfamiliy / Peroxisomal biogenesis protein family / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Peroxisome assembly protein 22 / Ubiquitin-conjugating enzyme E2-21 kDa
Similarity search - Component
Biological speciesPichia angusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsDanda, N. / Lunev, S. / Ali, A. / Groves, M.R. / Williams, C.
Funding support Netherlands, Qatar, 2items
OrganizationGrant numberCountry
NWO723.013.004 Netherlands
Qatar Research Leadership FoundationQatar
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural insights into K48-linked ubiquitin chain formation by the Pex4p-Pex22p complex.
Authors: Groves, M.R. / Schroer, C.F.E. / Middleton, A.J. / Lunev, S. / Danda, N. / Ali, A.M. / Marrink, S.J. / Williams, C.
History
DepositionApr 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2-21 kDa
D: Peroxin 22
C: Peroxin 22
B: Ubiquitin-conjugating enzyme E2-21 kDa


Theoretical massNumber of molelcules
Total (without water)74,5954
Polymers74,5954
Non-polymers00
Water00
1
A: Ubiquitin-conjugating enzyme E2-21 kDa
C: Peroxin 22


Theoretical massNumber of molelcules
Total (without water)37,2972
Polymers37,2972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-9 kcal/mol
Surface area14980 Å2
MethodPISA
2
D: Peroxin 22
B: Ubiquitin-conjugating enzyme E2-21 kDa


Theoretical massNumber of molelcules
Total (without water)37,2972
Polymers37,2972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-9 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.683, 61.582, 78.441
Angle α, β, γ (deg.)89.18, 78.02, 84.09
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALATYRTYRAA2 - 1834 - 185
21ALAALATYRTYRBD2 - 1834 - 185
12GLYGLYVALVALDB51 - 15329 - 131
22GLYGLYVALVALCC51 - 15329 - 131

NCS ensembles :
ID
1
2

-
Components

#1: Protein Ubiquitin-conjugating enzyme E2-21 kDa / E2 ubiquitin-conjugating enzyme PEX4 / Peroxin-4 / Ubiquitin carrier protein / Ubiquitin-protein ligase


Mass: 21671.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichia angusta (fungus) / Gene: PEX4 / Production host: Escherichia coli (E. coli)
References: UniProt: O60015, E2 ubiquitin-conjugating enzyme
#2: Protein Peroxin 22


Mass: 15625.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichia angusta (fungus) / Gene: PEX22 / Production host: Escherichia coli (E. coli) / References: UniProt: A2T0X6

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M BIS-TRIS Propane pH 7.8, 0.2 M sodium sulphate, 22 % w/v PEG-3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.85→48.0397 Å / Num. obs: 20450 / % possible obs: 95.02 % / Redundancy: 3.93 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 6.03
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 5.49 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 1822 / % possible all: 94.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Pex4:Pex22 complex coordinates from S. cerevisae (PDB: 2Y9M(Williams et al. 2012); 33/57 % and 14/35 % identity/similarity, respectively) as starting model

2y9m


Resolution: 2.85→48.0397 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.892 / SU B: 60.112 / SU ML: 0.475 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2837 980 5 %RANDOM
Rwork0.23608 ---
obs0.2385 18451 95.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 74.337 Å2
Baniso -1Baniso -2Baniso -3
1-2.85 Å2-0.04 Å2-2.49 Å2
2---0.81 Å25.69 Å2
3----3.15 Å2
Refinement stepCycle: 1 / Resolution: 2.85→48.0397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4639 0 0 0 4639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194763
X-RAY DIFFRACTIONr_bond_other_d0.0020.024469
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.9656471
X-RAY DIFFRACTIONr_angle_other_deg1.158310408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2815574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.01924.727220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.17315848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5921523
X-RAY DIFFRACTIONr_chiral_restr0.1190.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215181
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02918
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3274.4932302
X-RAY DIFFRACTIONr_mcbond_other2.3264.4922301
X-RAY DIFFRACTIONr_mcangle_it3.8266.7332874
X-RAY DIFFRACTIONr_mcangle_other3.8256.7342875
X-RAY DIFFRACTIONr_scbond_it2.1414.6932461
X-RAY DIFFRACTIONr_scbond_other2.144.6932462
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6576.9433598
X-RAY DIFFRACTIONr_long_range_B_refined6.05852.6335316
X-RAY DIFFRACTIONr_long_range_B_other6.05852.635317
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A114320.1
12B114320.1
21D61860.12
22C61860.12
LS refinement shellResolution: 2.78→2.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 64 -
Rwork0.453 1222 -
obs--87.48 %
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)
14.9994-0.0512-0.3593.3485-0.4317.4353-0.22840.49250.5508-0.19380.09780.1426-0.3797-0.25430.13060.0916-0.0346-0.00110.1456-0.10020.3438-1.318727.079410.7215
21.59760.8038-0.12462.40181.78136.1136-0.0764-0.32440.18220.02670.22430.0151-0.14840.2388-0.14780.043-0.02440.08610.2832-0.26680.36488.197125.773122.7209
34.1447-2.47630.15343.80580.4336.86170.32150.84530.7242-0.5048-0.30750.1681-0.5254-0.7798-0.0140.24130.0150.04040.5316-0.06540.653-8.515710.2549-3.2462
43.4337-2.6714-3.72167.2919-0.15336.1191-0.46330.0981-0.4257-0.06030.06830.64730.6046-0.18320.3950.1589-0.0525-0.00290.21-0.18650.2956-2.89132.61492.3558
52.10861.35692.15985.52174.26367.37150.09510.1898-0.1798-0.13220.08480.36540.3659-0.2186-0.17990.1471-0.06230.07020.1982-0.13070.3684-1.3249-9.8157-5.0388
66.3252-4.8482-3.14176.51313.4181.9252-0.1487-0.28290.04430.30520.16410.05060.13730.1329-0.01540.0384-0.05710.08370.1891-0.23160.29962.22836.64357.1187
76.5754-1.21690.98674.3356-0.88860.9420.18970.1561-0.18050.1163-0.0757-0.00180.25130.2755-0.1140.1994-0.00540.08940.1926-0.17250.19812.1947-9.1466-0.2209
85.19644.919-5.842612.759-9.785522.0142-0.01080.19890.0930.47470.3630.30470.1391-0.1222-0.35220.07710.0534-0.0090.2784-0.1780.202213.879332.593349.0897
914.5877-4.00071.38391.54440.53527.4085-0.4703-0.2179-0.70320.12830.156-0.1710.26420.03570.31430.2902-0.0280.07130.201-0.11590.56769.743136.153754.9576
105.2609-2.5773-2.68775.0371.2036.4171-0.1771-0.1951-0.02570.3830.20990.02050.14470.0523-0.03280.1922-0.0170.00450.2955-0.24560.2197.759629.484946.0633
111.3320.7294-2.744910.8487-7.97279.7579-0.0633-0.2187-0.1576-0.1448-0.06270.190.37380.39140.12610.3049-0.0102-0.00090.4568-0.2310.504819.800928.379649.0955
121.178-2.9887-0.52518.66390.09011.7583-0.0553-0.12750.0730.12190.1149-0.2546-0.04220.1967-0.05970.2876-0.0637-0.04480.48-0.02450.445723.881931.311146.9672
134.84031.4511-1.70995.03750.12036.8981-0.02190.2464-0.1929-0.01420.05580.10370.10960.0116-0.03390.0799-0.02970.05280.2011-0.24180.301419.3708-21.6337-11.4643
148.0910.6632-0.44087.0418-0.24950.0414-0.216-0.2198-0.41820.20940.1866-0.3026-0.03060.02720.02940.1344-0.06910.05830.22-0.19650.230419.9376-21.9813.536
155.1227-1.4738-1.09984.34246.17110.78030.05580.0720.06620.51140.0357-0.19671.1926-0.3402-0.09150.2283-0.0249-0.04460.27870.02090.398615.1591-31.24150.1264
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 67
2X-RAY DIFFRACTION2A68 - 183
3X-RAY DIFFRACTION3B2 - 51
4X-RAY DIFFRACTION4B52 - 78
5X-RAY DIFFRACTION5B79 - 119
6X-RAY DIFFRACTION6B120 - 149
7X-RAY DIFFRACTION7B150 - 183
8X-RAY DIFFRACTION8C51 - 61
9X-RAY DIFFRACTION9C62 - 70
10X-RAY DIFFRACTION10C71 - 120
11X-RAY DIFFRACTION11C121 - 133
12X-RAY DIFFRACTION12C134 - 155
13X-RAY DIFFRACTION13D50 - 106
14X-RAY DIFFRACTION14D107 - 140
15X-RAY DIFFRACTION15D141 - 154

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more