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- PDB-5lor: human NUDT22 -

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Basic information

Entry
Database: PDB / ID: 5lor
Titlehuman NUDT22
ComponentsNucleoside diphosphate-linked moiety X motif 22
KeywordsHYDROLASE / NUDIX
Function / homology
Function and homology information


GDP-mannose hydrolase activity / UDP-sugar diphosphatase / UDP-sugar diphosphatase activity / nucleoplasm / metal ion binding
Similarity search - Function
: / Nudix hydrolase domain profile. / NUDIX hydrolase domain
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCOSE / Uridine diphosphate glucose pyrophosphatase NUDT22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.192 Å
AuthorsCarter, M. / Stenmark, P.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Wenner-Gren Foundation Sweden
Swedish Cancer Society Sweden
CitationJournal: To Be Published
Title: Structural and functional studies of human NUDT22
Authors: Carter, M. / Ann-Sofie, J. / Patrick, H. / Puigvert, J.C. / Carranza, M.M. / Vallin, K.S.A. / Helleday, T. / Stenmark, P.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Nucleoside diphosphate-linked moiety X motif 22
B: Nucleoside diphosphate-linked moiety X motif 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6163
Polymers71,0502
Non-polymers5661
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-13 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.332, 46.565, 120.678
Angle α, β, γ (deg.)90.00, 94.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nucleoside diphosphate-linked moiety X motif 22 / Nudix motif 22


Mass: 35525.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT22, PP11246 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BRQ3
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 27.5% PEG3350, 0.1 M Bis Tris pH 5.25, 0.1 M ammonium sulfate, and 0.1 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.19→49.234 Å / Num. obs: 29705 / % possible obs: 98.2 % / Redundancy: 4.91 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.32
Reflection shellResolution: 2.19→2.31 Å / Redundancy: 4.94 % / Rmerge(I) obs: 1.032 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIXdev_1631refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NUDT22 apo

Resolution: 2.192→49.234 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 1510 5.08 %
Rwork0.2003 --
obs0.2028 29705 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.192→49.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4433 0 36 84 4553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094595
X-RAY DIFFRACTIONf_angle_d1.0746279
X-RAY DIFFRACTIONf_dihedral_angle_d13.9151663
X-RAY DIFFRACTIONf_chiral_restr0.044706
X-RAY DIFFRACTIONf_plane_restr0.005828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1916-2.26230.31791350.28432378X-RAY DIFFRACTION93
2.2623-2.34320.33471350.27532535X-RAY DIFFRACTION98
2.3432-2.4370.33571350.25572549X-RAY DIFFRACTION98
2.437-2.54790.29021290.24242546X-RAY DIFFRACTION99
2.5479-2.68220.31971470.23482567X-RAY DIFFRACTION99
2.6822-2.85030.27191450.23672532X-RAY DIFFRACTION99
2.8503-3.07030.29271120.22662628X-RAY DIFFRACTION99
3.0703-3.37920.26831290.21512583X-RAY DIFFRACTION99
3.3792-3.86810.25831380.19182596X-RAY DIFFRACTION99
3.8681-4.87270.18621700.15932575X-RAY DIFFRACTION99
4.8727-49.24660.20511350.17182706X-RAY DIFFRACTION99

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