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- PDB-4wzr: Crystal structure of human Puf-A -

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Basic information

Entry
Database: PDB / ID: 4wzr
TitleCrystal structure of human Puf-A
ComponentsPumilio domain-containing protein KIAA0020
KeywordsRNA BINDING PROTEIN / Pumilio repeat protein
Function / homology
Function and homology information


regulation of protein ADP-ribosylation / regulation of translation / chromosome / mRNA binding / nucleolus / endoplasmic reticulum / DNA binding / RNA binding / nucleoplasm
Similarity search - Function
CPL domain / Pumilio homologue 3 / CPL (NUC119) domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.154 Å
AuthorsQiu, C. / Hall, T.M.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Intramural Research Program United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization.
Authors: Qiu, C. / McCann, K.L. / Wine, R.N. / Baserga, S.J. / Hall, T.M.
History
DepositionNov 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
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_struct_oper_list.symmetry_operation
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pumilio domain-containing protein KIAA0020
B: Pumilio domain-containing protein KIAA0020
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5134
Polymers119,3292
Non-polymers1842
Water7,116395
1
A: Pumilio domain-containing protein KIAA0020
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7562
Polymers59,6641
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pumilio domain-containing protein KIAA0020
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7562
Polymers59,6641
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.495, 97.128, 282.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-818-

HOH

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Components

#1: Protein Pumilio domain-containing protein KIAA0020 / HBV X-transactivated gene 5 protein / HBV XAg-transactivated protein 5 / Minor histocompatibility ...HBV X-transactivated gene 5 protein / HBV XAg-transactivated protein 5 / Minor histocompatibility antigen HA-8 / HLA-HA8 / Puf-A


Mass: 59664.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0020, XTP5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15397
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20-25% PEG 3350, 0.2 M sodium malonate / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 68219 / % possible obs: 97.9 % / Redundancy: 7 % / Rsym value: 0.093 / Net I/σ(I): 19
Reflection shellResolution: 2.15→2.93 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.8 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.154→48.564 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 1998 2.93 %
Rwork0.1798 --
obs0.1811 68195 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.154→48.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8145 0 12 395 8552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078331
X-RAY DIFFRACTIONf_angle_d1.02211224
X-RAY DIFFRACTIONf_dihedral_angle_d13.1333219
X-RAY DIFFRACTIONf_chiral_restr0.0661294
X-RAY DIFFRACTIONf_plane_restr0.0041412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1543-2.20820.26941210.22653882X-RAY DIFFRACTION81
2.2082-2.26790.25461280.21174489X-RAY DIFFRACTION93
2.2679-2.33470.25071420.20374681X-RAY DIFFRACTION97
2.3347-2.410.27391470.19474710X-RAY DIFFRACTION99
2.41-2.49620.24261440.19284780X-RAY DIFFRACTION99
2.4962-2.59610.24661490.19224791X-RAY DIFFRACTION99
2.5961-2.71420.24051390.18894733X-RAY DIFFRACTION99
2.7142-2.85730.25841390.19464797X-RAY DIFFRACTION99
2.8573-3.03630.24481420.20664846X-RAY DIFFRACTION100
3.0363-3.27070.271460.19994788X-RAY DIFFRACTION100
3.2707-3.59970.24221460.17864858X-RAY DIFFRACTION100
3.5997-4.12040.20461490.16184859X-RAY DIFFRACTION100
4.1204-5.19030.18571460.15214929X-RAY DIFFRACTION100
5.1903-48.57630.20021600.1695054X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.9121.6108-3.93437.593-2.76015.00950.20610.09480.17530.4594-0.26380.28420.1307-0.16240.05670.3284-0.1181-0.03690.3341-0.02070.219987.2827105.6805161.8787
22.90380.81441.94021.14040.95951.5836-0.1205-0.07260.1225-0.15350.0516-0.0736-0.2530.02280.06280.4352-0.11010.06880.3222-0.0010.222961.910284.7645163.0667
31.7688-0.9111-1.83011.2251.46333.7052-0.04190.196-0.138-0.15750.0798-0.0796-0.12710.2357-0.02520.325-0.1550.02340.4434-0.03340.230962.307364.636126.9857
47.96590.5331-0.48061.80620.1865.0129-0.3174-0.0425-0.3024-0.34740.22840.42530.00180.06830.0950.3721-0.0996-0.13560.2854-0.01140.6016106.791792.147355.8592
52.17682.38090.4692.61690.41930.3152-0.41520.30060.15280.31330.1387-1.4074-0.21270.19110.18830.4207-0.0528-0.19610.33940.00820.717793.954680.945650.6286
60.94740.6391-0.70541.7961-1.26852.5597-0.07870.12960.008-0.13540.0286-0.00770.0689-0.09110.05010.1821-0.0443-0.02420.2616-0.05390.208279.327659.555457.1617
71.8679-0.2812-1.84260.62150.87973.34840.2875-0.20150.14260.0304-0.13120.1542-0.4549-0.0687-0.12080.3907-0.1220.04460.3079-0.0510.247860.469963.957791.5019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 131 through 211 )
2X-RAY DIFFRACTION2chain 'A' and (resid 212 through 374 )
3X-RAY DIFFRACTION3chain 'A' and (resid 375 through 646 )
4X-RAY DIFFRACTION4chain 'B' and (resid 127 through 179 )
5X-RAY DIFFRACTION5chain 'B' and (resid 180 through 248 )
6X-RAY DIFFRACTION6chain 'B' and (resid 249 through 399 )
7X-RAY DIFFRACTION7chain 'B' and (resid 400 through 646 )

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