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- PDB-4ynv: Assembly Chaperone of RpL4 (Acl4) (Residues 28-338) -

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Basic information

Entry
Database: PDB / ID: 4ynv
TitleAssembly Chaperone of RpL4 (Acl4) (Residues 28-338)
ComponentsACL4
KeywordsCHAPERONE / ribosome assembly / nucleocytoplasmic transport / tetratricopeptide repeat / ribosome biogenesis
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 / MAD / 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 1.3Apr 15, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / reflns
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _reflns.pdbx_Rmerge_I_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACL4
B: ACL4


Theoretical massNumber of molelcules
Total (without water)70,6182
Polymers70,6182
Non-polymers00
Water0
1
A: ACL4


Theoretical massNumber of molelcules
Total (without water)35,3091
Polymers35,3091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ACL4


Theoretical massNumber of molelcules
Total (without water)35,3091
Polymers35,3091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.487, 49.103, 80.051
Angle α, β, γ (deg.)98.66, 97.88, 100.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ACL4


Mass: 35308.801 Da / Num. of mol.: 2 / Fragment: UNP residues 27-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20 % (w/v) PEG 3350 0.2 M potassium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97936, 0.97961, 0.94937
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979361
20.979611
30.949371
ReflectionResolution: 2.95→20 Å / Num. obs: 30229 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.059 / Net I/σ(I): 22.4
Reflection shellResolution: 2.95→3 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.9 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.95→19.909 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 706 4.99 %Random selection
Rwork0.2273 ---
obs0.2288 30019 98.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→19.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4432 0 0 0 4432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044512
X-RAY DIFFRACTIONf_angle_d0.6986130
X-RAY DIFFRACTIONf_dihedral_angle_d13.9171684
X-RAY DIFFRACTIONf_chiral_restr0.035682
X-RAY DIFFRACTIONf_plane_restr0.007814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.0450.381380.39882633X-RAY DIFFRACTION98
3.045-3.15340.43041340.38072528X-RAY DIFFRACTION98
3.1534-3.27920.32791400.33882603X-RAY DIFFRACTION98
3.2792-3.42770.3341320.32152541X-RAY DIFFRACTION98
3.4277-3.60740.34711370.27522554X-RAY DIFFRACTION99
3.6074-3.83190.36621440.27042637X-RAY DIFFRACTION99
3.8319-4.12540.2681320.22272616X-RAY DIFFRACTION99
4.1254-4.53610.2111360.2012591X-RAY DIFFRACTION99
4.5361-5.18230.22861320.21112576X-RAY DIFFRACTION99
5.1823-6.49130.25941400.23472611X-RAY DIFFRACTION99
6.4913-19.90920.15751320.14812632X-RAY DIFFRACTION100

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