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- PDB-4pbd: Crystal structure of the N-terminal CS domain of human Shq1 -

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Basic information

Entry
Database: PDB / ID: 4pbd
TitleCrystal structure of the N-terminal CS domain of human Shq1
ComponentsProtein SHQ1 homolog
KeywordsPROTEIN BINDING / CS domain / Shq1 / dyskerin / Cbf5 / telomerase / H/ACA
Function / homology
Function and homology information


box H/ACA snoRNP assembly / negative regulation of rRNA processing / positive regulation of telomerase RNA localization to Cajal body / Telomere Extension By Telomerase / protein-RNA complex assembly / unfolded protein binding / positive regulation of apoptotic process / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Shq1 protein domain / Protein Shq1 / : / SHQ1 protein, Shq1 domain / SHQ1-like, CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Immunoglobulin-like ...Shq1 protein domain / Protein Shq1 / : / SHQ1 protein, Shq1 domain / SHQ1-like, CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein SHQ1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å
Model detailsCrystal structure of the N-terminal CS domain of human Shq1
AuthorsSingh, M. / Wang, Z. / Cascio, D. / Feigon, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM048123 United States
National Science Foundation (NSF, United States)MCB1022379 United States
Department of Energy (DOE, United States)DE-FC0302ER63421 United States
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structure and Interactions of the CS Domain of Human H/ACA RNP Assembly Protein Shq1.
Authors: Singh, M. / Wang, Z. / Cascio, D. / Feigon, J.
History
DepositionApr 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein SHQ1 homolog


Theoretical massNumber of molelcules
Total (without water)12,7411
Polymers12,7411
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.610, 41.610, 132.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Protein SHQ1 homolog


Mass: 12740.834 Da / Num. of mol.: 1 / Fragment: CS domain (UNP residues 1-96)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHQ1 / Plasmid: pET46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6PI26
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 0.2 M ammonium tartrate dibasic, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2011
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.68→39.69 Å / Num. obs: 24666 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4.56 % / Biso Wilson estimate: 19.83 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.077 / Χ2: 1.444 / Net I/σ(I): 19.07 / Num. measured all: 112617
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.68-1.720.7580.5612.48154188318600.63598.8
1.72-1.770.8360.4443.167959180517920.50399.3
1.77-1.820.8870.354.027935177817600.39699
1.82-1.880.9240.295.267829171917060.3399.2
1.88-1.940.9510.2097.855548164914550.24488.2
1.94-2.010.9690.179.557366161715930.19398.5
2.01-2.080.9730.14510.956501156815170.16896.7
2.08-2.170.9850.11312.756988151414890.12898.3
2.17-2.270.980.10113.865551141813090.11992.3
2.27-2.380.9890.08915.036122136513120.10196.1
2.38-2.50.9910.07917.026406130012920.08999.4
2.5-2.660.9930.07217.876147124712440.08199.8
2.66-2.840.9930.06920.355572115411520.07899.8
2.84-3.070.9950.05623.315281108710840.06399.7
3.07-3.360.9960.05324.4747289869840.05999.8
3.36-3.760.9950.05424.9439409108950.06198.4
3.76-4.340.9960.04825.5235087877790.05499
4.34-5.310.9980.03627.1233146746690.0499.3
5.31-7.510.9980.03427.225895105090.03799.8
7.510.9950.03225.3811792882650.03792

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Phasing

PhasingMethod: SAD
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 13543
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.43-10031.90.738502
4.22-5.4326.60.806501
3.66-4.2228.10.785508
3.3-3.6626.70.806506
3.05-3.330.70.831510
2.86-3.0531.30.782502
2.71-2.8633.90.775509
2.59-2.7139.10.736507
2.48-2.5934.60.749507
2.39-2.4833.30.782501
2.31-2.3932.20.782505
2.24-2.3131.90.758517
2.18-2.2438.20.71520
2.12-2.1834.80.741536
2.07-2.1235.50.738550
2.02-2.0739.60.666569
1.97-2.0234.80.699570
1.93-1.9737.60.68601
1.89-1.9338.80.682588
1.85-1.8947.30.622621
1.81-1.8541.60.682619
1.78-1.8140.90.683636
1.75-1.7845.90.64647
1.7-1.7546.10.5941011

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASER2.5.5phasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.68→25.877 Å / FOM work R set: 0.8236 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 687 4.96 %
Rwork0.2036 13172 -
obs0.2055 13859 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.18 Å2 / Biso mean: 26.31 Å2 / Biso min: 9.79 Å2
Refinement stepCycle: final / Resolution: 1.68→25.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 0 165 991
Biso mean---36.06 -
Num. residues----102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007852
X-RAY DIFFRACTIONf_angle_d1.1421154
X-RAY DIFFRACTIONf_chiral_restr0.045120
X-RAY DIFFRACTIONf_plane_restr0.006151
X-RAY DIFFRACTIONf_dihedral_angle_d13305
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6803-1.810.3091390.226425832722100
1.81-1.99210.24121280.23952545267398
1.9921-2.28020.29261360.232578271498
2.2802-2.87220.23831460.222226392785100
2.8722-25.88040.2191380.17552827296599
Refinement TLS params.Method: refined / Origin x: -1.2816 Å / Origin y: 16.4426 Å / Origin z: -7.6047 Å
111213212223313233
T0.1134 Å2-0.0418 Å2-0.0122 Å2-0.1396 Å20.0011 Å2--0.1225 Å2
L0.298 °2-0.2512 °2-0.0923 °2-0.2104 °20.0814 °2--0.3283 °2
S-0.0439 Å °0.0833 Å °0.0533 Å °-0.0145 Å °0.0461 Å °0.0288 Å °0.0018 Å °0.0387 Å °-0.0003 Å °
Refinement TLS groupSelection details: all

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