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- PDB-4ynw: Assembly Chaperone of RpL4 (Acl4) (Residues 1-338) -

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Basic information

Entry
Database: PDB / ID: 4ynw
TitleAssembly Chaperone of RpL4 (Acl4) (Residues 1-338)
ComponentsACL4
KeywordsCHAPERONE / ribosome assembly / nucleocytoplasmic transport / tetratricopeptide repeat
Function / homologyTetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Uncharacterized protein
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsHuber, F.M. / Hoelz, A.
CitationJournal: Mol.Cell / Year: 2015
Title: Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribosome Is Regulated by Its Eukaryote-Specific Extension.
Authors: Stelter, P. / Huber, F.M. / Kunze, R. / Flemming, D. / Hoelz, A. / Hurt, E.
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACL4
B: ACL4


Theoretical massNumber of molelcules
Total (without water)76,1712
Polymers76,1712
Non-polymers00
Water00
1
A: ACL4


Theoretical massNumber of molelcules
Total (without water)38,0861
Polymers38,0861
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ACL4


Theoretical massNumber of molelcules
Total (without water)38,0861
Polymers38,0861
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.134, 49.566, 80.314
Angle α, β, γ (deg.)98.59, 100.11, 98.53
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ACL4


Mass: 38085.727 Da / Num. of mol.: 2 / Fragment: UNP residues 1-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0010130 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0I4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 % (w/v) PEG 3350, 0.2 M ammonium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97939 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 16367 / % possible obs: 97.2 % / Redundancy: 7.7 % / Rsym value: 0.046 / Net I/σ(I): 40.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2 / % possible all: 85.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YNV

4ynv


Resolution: 2.95→19.616 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2667 1508 10.08 %Random selection
Rwork0.2349 ---
obs0.2382 14964 98.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→19.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4432 0 0 0 4432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034512
X-RAY DIFFRACTIONf_angle_d0.666130
X-RAY DIFFRACTIONf_dihedral_angle_d12.5911684
X-RAY DIFFRACTIONf_chiral_restr0.03682
X-RAY DIFFRACTIONf_plane_restr0.007814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.04490.43841350.36451157X-RAY DIFFRACTION93
3.0449-3.15330.38811320.33321205X-RAY DIFFRACTION97
3.1533-3.2790.45221450.34171236X-RAY DIFFRACTION98
3.279-3.42750.38541340.31011202X-RAY DIFFRACTION98
3.4275-3.60710.37791330.29861236X-RAY DIFFRACTION99
3.6071-3.83150.34371410.29411260X-RAY DIFFRACTION99
3.8315-4.12480.29841420.26661221X-RAY DIFFRACTION99
4.1248-4.53530.33411330.23841230X-RAY DIFFRACTION99
4.5353-5.1810.29461340.24291223X-RAY DIFFRACTION99
5.181-6.4880.27461390.26481256X-RAY DIFFRACTION100
6.488-19.61610.15791400.15291230X-RAY DIFFRACTION99

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