[English] 日本語
Yorodumi
- PDB-2wl8: X-ray crystal structure of Pex19p -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wl8
TitleX-ray crystal structure of Pex19p
ComponentsPEROXISOMAL BIOGENESIS FACTOR 19
KeywordsPROTEIN TRANSPORT / BIOGENESIS DISORDER / ZELLWEGER SYNDROME / MEMBRANE / PRENYLATION
Function / homology
Function and homology information


peroxisome membrane biogenesis / peroxisome membrane class-1 targeting sequence binding / establishment of protein localization to peroxisome / negative regulation of lipid binding / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / protein targeting to peroxisome / Class I peroxisomal membrane protein import / peroxisome organization / protein carrier chaperone ...peroxisome membrane biogenesis / peroxisome membrane class-1 targeting sequence binding / establishment of protein localization to peroxisome / negative regulation of lipid binding / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / protein targeting to peroxisome / Class I peroxisomal membrane protein import / peroxisome organization / protein carrier chaperone / ABC transporters in lipid homeostasis / peroxisome fission / peroxisomal membrane / : / brush border membrane / peroxisome / ATPase binding / protein stabilization / protein-containing complex / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Pex19, mPTS binding domain / Pex19 protein / Pex19, C-terminal domain superfamily / Pex19 protein family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Peroxisomal biogenesis factor 19
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.05 Å
AuthorsSchueller, N. / Holton, S.J. / Stanley, W.A. / Song, Y.H. / Konarev, P. / Roessle, M. / Erdmann, R. / Schliebs, W. / Wilmanns, M.
CitationJournal: Embo J. / Year: 2010
Title: The Peroxisomal Receptor Pex19P Forms a Helical Mpts Recognition Domain.
Authors: Schueller, N. / Holton, S.J. / Fodor, K. / Milewski, M. / Konarev, P. / Stanley, W.A. / Wolf, J. / Erdmann, R. / Schliebs, W. / Song, Y.H. / Wilmanns, M.
History
DepositionJun 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PEROXISOMAL BIOGENESIS FACTOR 19
B: PEROXISOMAL BIOGENESIS FACTOR 19
C: PEROXISOMAL BIOGENESIS FACTOR 19
D: PEROXISOMAL BIOGENESIS FACTOR 19


Theoretical massNumber of molelcules
Total (without water)57,4734
Polymers57,4734
Non-polymers00
Water3,423190
1
A: PEROXISOMAL BIOGENESIS FACTOR 19


Theoretical massNumber of molelcules
Total (without water)14,3681
Polymers14,3681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PEROXISOMAL BIOGENESIS FACTOR 19


Theoretical massNumber of molelcules
Total (without water)14,3681
Polymers14,3681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PEROXISOMAL BIOGENESIS FACTOR 19


Theoretical massNumber of molelcules
Total (without water)14,3681
Polymers14,3681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PEROXISOMAL BIOGENESIS FACTOR 19


Theoretical massNumber of molelcules
Total (without water)14,3681
Polymers14,3681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.150, 91.120, 122.287
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
PEROXISOMAL BIOGENESIS FACTOR 19 / PEROXIN-19 / PEROXISOMAL FARNESYLATED PROTEIN / 33 KDA HOUSEKEEPING PROTEIN


Mass: 14368.188 Da / Num. of mol.: 4 / Fragment: RESIDUES 161-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40855
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.53 % / Description: NONE
Crystal growDetails: 2.0M SODIUM MALONATE, PH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9792
DetectorType: MARRESEARCH SX-165 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→54.47 Å / Num. obs: 45015 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.22 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.57
Reflection shellResolution: 2.18→2.2 Å / Mean I/σ(I) obs: 2.69

-
Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOSFLMdata reduction
TRUNCATEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.05→49.45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.13 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23886 2400 5.1 %RANDOM
Rwork0.19921 ---
obs0.20118 45015 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.368 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2---0.14 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.05→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 0 0 190 3715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223608
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0931.9954881
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.82426.667177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.3215689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.751158
X-RAY DIFFRACTIONr_chiral_restr0.1750.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0222729
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1921.52185
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.20723571
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.01831423
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.3324.51310
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 183 -
Rwork0.269 3274 -
obs--98.63 %
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)
13.0418-0.2061-0.19352.9783-1.1253.37510.0007-0.03290.00980.14860.0640.03630.0517-0.0288-0.06470.0258-0.0059-0.00260.0088-0.0090.07177.791340.539995.0986
24.2522-1.3181.94351.6569-0.6451.6556-0.0097-0.00610.21610.0128-0.0998-0.2204-0.0210.09340.10960.07450.00860.0540.05320.02310.134639.060437.997690.7355
32.2379-0.2446-0.38553.298-0.02451.96440.08390.07590.0959-0.3012-0.1139-0.0492-0.01490.08270.030.0603-0.0072-0.00220.0293-0.00070.055222.665659.184681.5319
43.8151-1.26470.87594.9027-0.74476.051-0.2966-0.51680.2680.77320.29810.3532-0.8979-1.0064-0.00150.24230.21490.05430.30090.01020.2599-7.708957.437199.0081
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A171 - 280
2X-RAY DIFFRACTION2B171 - 274
3X-RAY DIFFRACTION3C171 - 279
4X-RAY DIFFRACTION4D171 - 279

+
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://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