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- PDB-1sqw: Crystal structure of KD93, a novel protein expressed in the human pro -

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Basic information

Entry
Database: PDB / ID: 1sqw
TitleCrystal structure of KD93, a novel protein expressed in the human pro
ComponentsSaccharomyces cerevisiae Nip7p homolog
KeywordsUNKNOWN FUNCTION / PUA
Function / homology
Function and homology information


preribosome, large subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / ribosomal large subunit biogenesis / ribosome assembly / nucleolus / RNA binding / nucleoplasm / cytosol
Similarity search - Function
Nuclear Transport Factor 2; Chain: A, - #220 / Ribosome biogenesis factor, NIP7 / UPF0113, pre-PUA domain / UPF0113 Pre-PUA domain / UPF0113, PUA domain / UPF0113 PUA domain / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain ...Nuclear Transport Factor 2; Chain: A, - #220 / Ribosome biogenesis factor, NIP7 / UPF0113, pre-PUA domain / UPF0113 Pre-PUA domain / UPF0113, PUA domain / UPF0113 PUA domain / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / PUA-like superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
60S ribosome subunit biogenesis protein NIP7 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsLiu, J.F. / Wang, X.Q. / Wang, Z.X. / Chen, J.R. / Jiang, T. / An, X.M. / Chan, W.R. / Liang, D.C.
CitationJournal: J.Struct.Biol. / Year: 2004
Title: Crystal structure of KD93, a novel protein expressed in human hematopoietic stem/progenitor cells.
Authors: Liu, J.F. / Wang, X.Q. / Wang, Z.X. / Chen, J.R. / Jiang, T. / An, X.M. / Chang, W.R. / Liang, D.C.
History
DepositionMar 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Saccharomyces cerevisiae Nip7p homolog


Theoretical massNumber of molelcules
Total (without water)21,5631
Polymers21,5631
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.203, 57.203, 132.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Saccharomyces cerevisiae Nip7p homolog


Mass: 21562.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: novel protein expressed in human hematopoietic stem/progenitor cells
Source: (gene. exp.) Homo sapiens (human) / Gene: novel gene / Plasmid: pET-kd93 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: Q9Y221
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 28% PEG 4000, 0.2M MgCl2, 0.1M sodium acetate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 0.9793, 0.9799, 0.9712
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97991
30.97121
ReflectionResolution: 1.9→50 Å / Num. obs: 17749 / % possible obs: 98.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→6 Å /
RfactorNum. reflection
Rfree0.261 -
Rwork0.225 -
obs-15378
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.163 Å20 Å20 Å2
2--0.163 Å20 Å2
3----0.327 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 0 131 1540
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010973
X-RAY DIFFRACTIONc_angle_deg1.41766
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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