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- PDB-8bdu: H33 variant of DoBi scaffold based on PIH1D1 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 8bdu
TitleH33 variant of DoBi scaffold based on PIH1D1 N-terminal domain
ComponentsPIH1 domain-containing protein 1
KeywordsPROTEIN BINDING / protein-protein recognition / ribosome display / IL-10 / cytokine
Function / homology
Function and homology information


TORC1 complex assembly / snoRNA localization / positive regulation of glucose mediated signaling pathway / pre-snoRNP complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / R2TP complex / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / RPAP3/R2TP/prefoldin-like complex / box C/D snoRNP assembly / positive regulation of TORC1 signaling ...TORC1 complex assembly / snoRNA localization / positive regulation of glucose mediated signaling pathway / pre-snoRNP complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / R2TP complex / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / RPAP3/R2TP/prefoldin-like complex / box C/D snoRNP assembly / positive regulation of TORC1 signaling / epithelial cell differentiation / histone reader activity / phosphoprotein binding / positive regulation of protein serine/threonine kinase activity / rRNA processing / histone binding / ATPase binding / protein stabilization / chromatin remodeling / ribonucleoprotein complex / nucleolus / protein kinase binding / nucleus / cytoplasm
Similarity search - Function
PIH1D1/2/3, CS-like domain / PIH1 CS-like domain / PIH1, N-terminal / PIH1 N-terminal domain
Similarity search - Domain/homology
PIH1 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.471 Å
AuthorsKolenko, P. / Mikulecky, P. / Pham, P.N. / Schneider, B.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/0.0/16_019/0000778 Czech Republic
CitationJournal: J.Appl.Crystallogr. / Year: 2023
Title: Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10.
Authors: Kolenko, P. / Mikulecky, P. / Pham, P.N. / Maly, M. / Schneider, B.
History
DepositionOct 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PIH1 domain-containing protein 1
B: PIH1 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)34,1492
Polymers34,1492
Non-polymers00
Water00
1
A: PIH1 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)17,0741
Polymers17,0741
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PIH1 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)17,0741
Polymers17,0741
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.131, 123.131, 190.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein PIH1 domain-containing protein 1 / Nucleolar protein 17 homolog


Mass: 17074.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIH1D1, NOP17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NWS0

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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 % sol: 76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1 M (NH4)2SO4 1% (w/v) PEG3350 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.47→47.53 Å / Num. obs: 18374 / % possible obs: 69 % / Redundancy: 12.6 % / CC1/2: 0.999 / CC star: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.036 / Rrim(I) all: 0.136 / Net I/σ(I): 14.8
Reflection shellResolution: 2.47→2.71 Å / Redundancy: 12.6 % / Rmerge(I) obs: 3.429 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 919 / CC1/2: 0.224 / CC star: 0.605 / Rpim(I) all: 1.216 / Rrim(I) all: 3.846 / % possible all: 14.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AVC

7avc


Resolution: 2.471→47.53 Å / Cor.coef. Fo:Fc: 0.94 / SU B: 15.215 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281
Details: Hydrogens have been added in their riding positions, the last cycles of refinement performed using all reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 910 5 %Random selection
Rwork0.219 18374 --
all0.222 ---
obs0.223 18374 69.158 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 81.639 Å2
Baniso -1Baniso -2Baniso -3
1-0.299 Å2-0 Å2-0 Å2
2--0.299 Å2-0 Å2
3----0.599 Å2
Refinement stepCycle: LAST / Resolution: 2.471→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 0 0 2071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122122
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161910
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.6392874
X-RAY DIFFRACTIONr_angle_other_deg0.5721.5514479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.028512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.43510356
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.6061095
X-RAY DIFFRACTIONr_chiral_restr0.0790.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022411
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
X-RAY DIFFRACTIONr_nbd_refined0.2180.2435
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.21826
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21059
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.21205
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.224
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.25
X-RAY DIFFRACTIONr_nbd_other0.1870.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2280.21
X-RAY DIFFRACTIONr_mcbond_it9.9218.1081062
X-RAY DIFFRACTIONr_mcbond_other9.8968.111062
X-RAY DIFFRACTIONr_mcangle_it14.03712.2011324
X-RAY DIFFRACTIONr_mcangle_other14.05612.2061325
X-RAY DIFFRACTIONr_scbond_it9.4668.671060
X-RAY DIFFRACTIONr_scbond_other9.4628.6771061
X-RAY DIFFRACTIONr_scangle_it13.48112.7421550
X-RAY DIFFRACTIONr_scangle_other13.47712.7491551
X-RAY DIFFRACTIONr_lrange_it19.353155.6618483
X-RAY DIFFRACTIONr_lrange_other19.356155.6428483
LS refinement shellResolution: 2.471→2.535 Å
RfactorNum. reflection% reflection
Rwork0.494 106 -
Rfree-0 -
obs--5.4894 %

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