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- PDB-1wlf: Structure of the N-terminal domain of PEX1 AAA-ATPase: Characteri... -

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Basic information

Entry
Database: PDB / ID: 1wlf
TitleStructure of the N-terminal domain of PEX1 AAA-ATPase: Characterization of a putative adaptor-binding domain
ComponentsPeroxisome biogenesis factor 1
KeywordsPROTEIN TRANSPORT / N-TERMINAL DOMAIN
Function / homology
Function and homology information


microtubule-based peroxisome localization / protein targeting to peroxisome / protein import into peroxisome matrix / peroxisome organization / : / Peroxisomal protein import / peroxisomal membrane / peroxisome / lipid binding / protein-containing complex binding ...microtubule-based peroxisome localization / protein targeting to peroxisome / protein import into peroxisome matrix / peroxisome organization / : / Peroxisomal protein import / peroxisomal membrane / peroxisome / lipid binding / protein-containing complex binding / ATP hydrolysis activity / ATP binding / cytoplasm / cytosol
Similarity search - Function
Peroxisome biogenesis factor 1, N-terminal, alpha/beta / Peroxisome biogenesis factor 1, N-terminal / Peroxisome biogenesis factor 1 / Peroxisome biogenesis factor 1, N-terminal, psi beta-barrel fold / Peroxisome biogenesis factor 1, N-terminal / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / CDC48 domain 2-like superfamily ...Peroxisome biogenesis factor 1, N-terminal, alpha/beta / Peroxisome biogenesis factor 1, N-terminal / Peroxisome biogenesis factor 1 / Peroxisome biogenesis factor 1, N-terminal, psi beta-barrel fold / Peroxisome biogenesis factor 1, N-terminal / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Peroxisome biogenesis factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.05 Å
AuthorsShiozawa, K. / Maita, N. / Tomii, K. / Seto, A. / Goda, N. / Tochio, H. / Akiyama, Y. / Shimizu, T. / Shirakawa, M. / Hiroaki, H.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure of the N-terminal Domain of PEX1 AAA-ATPase: CHARACTERIZATION OF A PUTATIVE ADAPTOR-BINDING DOMAIN
Authors: Shiozawa, K. / Maita, N. / Tomii, K. / Seto, A. / Goda, N. / Akiyama, Y. / Shimizu, T. / Shirakawa, M. / Hiroaki, H.
History
DepositionJun 25, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: refine_ls_shell
Item: _refine_ls_shell.number_reflns_obs / _refine_ls_shell.percent_reflns_obs
Revision 1.4Nov 6, 2019Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value
Revision 1.5Mar 13, 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

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Assembly

Deposited unit
A: Peroxisome biogenesis factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0882
Polymers19,9921
Non-polymers961
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.560, 63.560, 33.514
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Peroxisome biogenesis factor 1 / PEX1


Mass: 19991.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5BL07
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG4000, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 30, 2004 / Details: osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 52572 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 32.58 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 5.4
Reflection shellResolution: 2.05→2.15 Å / % possible obs: 99.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 0.25 / Num. unique all: 1353 / Rsym value: 0.23

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIR / Resolution: 2.05→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 771 -RANDOM
Rwork0.2134 ---
all-9449 --
obs-9434 99.8 %-
Refinement stepCycle: LAST / Resolution: 2.05→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 5 51 1351
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d24.46
X-RAY DIFFRACTIONc_improper_angle_d0.809
LS refinement shellResolution: 2.05→2.12 Å
RfactorNum. reflection
Rfree0.3203 78
Rwork0.2463 -
obs-928

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