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- PDB-3o7x: Crystal structure of human Hili PAZ domain -

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Basic information

Entry
Database: PDB / ID: 3o7x
TitleCrystal structure of human Hili PAZ domain
ComponentsPiwi-like protein 2
KeywordsRNA BINDING PROTEIN / Piwi / RNA silencing / pi-RNA / Hiwi1 / Hili / PAZ domain
Function / homology
Function and homology information


siRNA-mediated retrotransposon silencing by heterochromatin formation / perinucleolar chromocenter / retrotransposon silencing by mRNA destabilization / PET complex / pi-body / secondary piRNA processing / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / retrotransposon silencing by heterochromatin formation / positive regulation of meiosis I ...siRNA-mediated retrotransposon silencing by heterochromatin formation / perinucleolar chromocenter / retrotransposon silencing by mRNA destabilization / PET complex / pi-body / secondary piRNA processing / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / retrotransposon silencing by heterochromatin formation / positive regulation of meiosis I / : / germ-line stem cell population maintenance / negative regulation of circadian rhythm / chromatoid body / dense body / P granule / regulatory ncRNA-mediated gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / oogenesis / PIWI-interacting RNA (piRNA) biogenesis / RNA endonuclease activity / positive regulation of translation / meiotic cell cycle / rhythmic process / spermatogenesis / mRNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
paz domain / paz domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily ...paz domain / paz domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain / PAZ domain profile. / Beta Complex / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9248 Å
AuthorsTian, Y. / Simanshu, D.K. / Ma, J.-B. / Patel, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Inaugural Article: Structural basis for piRNA 2'-O-methylated 3'-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains.
Authors: Tian, Y. / Simanshu, D.K. / Ma, J.B. / Patel, D.J.
History
DepositionAug 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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: Piwi-like protein 2
B: Piwi-like protein 2
C: Piwi-like protein 2
D: Piwi-like protein 2


Theoretical massNumber of molelcules
Total (without water)65,6874
Polymers65,6874
Non-polymers00
Water1629
1
A: Piwi-like protein 2

A: Piwi-like protein 2


Theoretical massNumber of molelcules
Total (without water)32,8432
Polymers32,8432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area2540 Å2
ΔGint-30 kcal/mol
Surface area13940 Å2
MethodPISA
2
B: Piwi-like protein 2
C: Piwi-like protein 2


Theoretical massNumber of molelcules
Total (without water)32,8432
Polymers32,8432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-30 kcal/mol
Surface area12280 Å2
MethodPISA
3
D: Piwi-like protein 2

D: Piwi-like protein 2


Theoretical massNumber of molelcules
Total (without water)32,8432
Polymers32,8432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_856-x+3,y,-z+3/21
Buried area2280 Å2
ΔGint-29 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.535, 142.949, 226.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 16:89 or resseq 106:114 )A16 - 89
121chain A and (resseq 16:89 or resseq 106:114 )A106 - 114
211chain B and (resseq 16:89 or resseq 106:114 )B16 - 89
221chain B and (resseq 16:89 or resseq 106:114 )B106 - 114
311chain C and (resseq 16:89 or resseq 106:114 )C16 - 89
321chain C and (resseq 16:89 or resseq 106:114 )C106 - 114
411chain D and (resseq 16:89 or resseq 106:114 )D16 - 89
421chain D and (resseq 16:89 or resseq 106:114 )D106 - 114

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Components

#1: Protein
Piwi-like protein 2 / Cancer/testis antigen 80 / CT80


Mass: 16421.713 Da / Num. of mol.: 4 / Fragment: PAZ domain (UNP Residues 389-525)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIWIL2, HILI / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8TC59
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 50.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 4-8% PEG4000 and 50 mM MgSO4 in 50 mM MES buffer, pH 5.6 to 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
Details: Cryogenically-cooled single crystal Si(111) side bounce monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 5.9 % / Av σ(I) over netI: 20.23 / Number: 78673 / Rmerge(I) obs: 0.081 / Χ2: 1.54 / D res high: 3 Å / D res low: 30 Å / Num. obs: 13333 / % possible obs: 97.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.443099.510.0573.9025.8
5.126.4410010.0731.8036.2
4.485.1210010.0561.5246.3
4.074.4810010.0611.1926.4
3.784.0799.910.0951.0936.4
3.563.7810010.1341.0756.4
3.383.5610010.181.1046.3
3.233.3898.510.2181.0715.7
3.113.2396.710.2371.0744.9
33.1180.210.2691.2294.1
ReflectionResolution: 2.92→50 Å / Num. obs: 14092 / % possible obs: 95.1 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.091 / Χ2: 1.103 / Net I/σ(I): 20.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.92-3.024.70.30739720.90967.2
3.02-3.155.30.28212390.9686
3.15-3.296.20.25514220.96898.3
3.29-3.467.30.22514451.05799.1
3.46-3.687.80.16814771.115100
3.68-3.967.80.11314591.157100
3.96-4.367.90.08414741.14100
4.36-4.997.70.06914951.086100
4.99-6.297.30.07315011.22499.9
6.29-506.30.05316081.20499.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
PHENIX1.4_153refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9248→44.385 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / σ(F): 0.06 / Phase error: 32.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2934 1332 9.98 %
Rwork0.2459 --
obs0.2506 13346 90.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.941 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 135.33 Å2 / Biso mean: 75.2692 Å2 / Biso min: 29.25 Å2
Baniso -1Baniso -2Baniso -3
1-15.3214 Å20 Å2-0 Å2
2--14.8512 Å20 Å2
3----30.1726 Å2
Refinement stepCycle: LAST / Resolution: 2.9248→44.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 0 9 3587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053648
X-RAY DIFFRACTIONf_angle_d0.8874938
X-RAY DIFFRACTIONf_chiral_restr0.052551
X-RAY DIFFRACTIONf_plane_restr0.003637
X-RAY DIFFRACTIONf_dihedral_angle_d15.5321340
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A690X-RAY DIFFRACTIONPOSITIONAL0.057
12B690X-RAY DIFFRACTIONPOSITIONAL0.057
13C690X-RAY DIFFRACTIONPOSITIONAL0.061
14D694X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9248-3.02940.4515730.349171178455
3.0294-3.15060.36751100.3188951106173
3.1506-3.2940.38171250.29151162128789
3.294-3.46760.32261330.29581216134993
3.4676-3.68470.33161460.26981273141996
3.6847-3.96910.32321410.25721278141997
3.9691-4.36820.27211450.2151310145599
4.3682-4.99950.22911510.19491334148599
4.9995-6.2960.24131490.225913431492100
6.296-44.39050.28891590.235614361595100

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