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- PDB-5lf9: Crystal structure of human NUDT22 -

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Basic information

Entry
Database: PDB / ID: 5lf9
TitleCrystal structure of human NUDT22
ComponentsNucleoside diphosphate-linked moiety X motif 22
KeywordsTRANSFERASE / Nucleoside diphosphate-linked moiety X motif 22 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology: / GDP-mannose hydrolase activity / UDP-sugar diphosphatase / UDP-sugar diphosphatase activity / Nudix hydrolase domain profile. / NUDIX hydrolase domain / nucleoplasm / metal ion binding / Uridine diphosphate glucose pyrophosphatase NUDT22
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsTallant, C. / Siejka, P. / Mathea, S. / Shrestha, L. / Krojer, T. / Srikannathasan, V. / Elkins, J.M. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. ...Tallant, C. / Siejka, P. / Mathea, S. / Shrestha, L. / Krojer, T. / Srikannathasan, V. / Elkins, J.M. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Huber, K. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of human NUDT22
Authors: Tallant, C. / Siejka, P. / Mathea, S. / Shrestha, L. / Krojer, T. / Srikannathasan, V. / Elkins, J.M. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Huber, K.
History
DepositionJun 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 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

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Assembly

Deposited unit
A: Nucleoside diphosphate-linked moiety X motif 22


Theoretical massNumber of molelcules
Total (without water)32,7071
Polymers32,7071
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.810, 52.114, 101.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 32706.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT22, PP11246 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BRQ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.02 Å3/Da / Density % sol: 39.18 % / Description: Rod
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% HighPEG, 0.1 M hepes pH 7.5, 0.1 M NaKPO, 10% EDO
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.45→29.39 Å / Num. obs: 47830 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 19.304 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.024 / Net I/σ(I): 15
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.005 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→29.39 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.002 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20705 2378 5 %RANDOM
Rwork0.17099 ---
obs0.17283 45389 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.884 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å2-0 Å2
2---1.3 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.45→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 0 91 2250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192253
X-RAY DIFFRACTIONr_bond_other_d0.0020.022121
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.973080
X-RAY DIFFRACTIONr_angle_other_deg1.01534885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0945290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70323.96101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11615351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2571517
X-RAY DIFFRACTIONr_chiral_restr0.1050.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02513
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.582.361148
X-RAY DIFFRACTIONr_mcbond_other2.5112.3571147
X-RAY DIFFRACTIONr_mcangle_it3.0623.5291439
X-RAY DIFFRACTIONr_mcangle_other3.0653.5321440
X-RAY DIFFRACTIONr_scbond_it3.1922.7411105
X-RAY DIFFRACTIONr_scbond_other3.1912.7431106
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4393.9791641
X-RAY DIFFRACTIONr_long_range_B_refined3.95629.4412407
X-RAY DIFFRACTIONr_long_range_B_other3.94829.2732388
X-RAY DIFFRACTIONr_rigid_bond_restr3.05834374
X-RAY DIFFRACTIONr_sphericity_free16.57528
X-RAY DIFFRACTIONr_sphericity_bonded7.93754380
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 178 -
Rwork0.23 3265 -
obs--99.48 %

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