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- PDB-5lou: human NUDT22 -

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Basic information

Entry
Database: PDB / ID: 5lou
Titlehuman NUDT22
ComponentsNucleoside diphosphate-linked moiety X motif 22
KeywordsHYDROLASE / NUDIX
Function / homologyGDP-mannose hydrolase activity / UDP-sugar diphosphatase / UDP-sugar diphosphatase activity / Nudix hydrolase domain profile. / NUDIX hydrolase domain / nucleoplasm / metal ion binding / PHOSPHATE ION / Uridine diphosphate glucose pyrophosphatase NUDT22
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.8 Å
AuthorsCarter, M. / Stenmark, P.
CitationJournal: Structure / Year: 2018
Title: Human NUDT22 Is a UDP-Glucose/Galactose Hydrolase Exhibiting a Unique Structural Fold.
Authors: Carter, M. / Jemth, A.S. / Carreras-Puigvert, J. / Herr, P. / Martinez Carranza, M. / Vallin, K.S.A. / Throup, A. / Helleday, T. / Stenmark, P.
History
DepositionAug 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3May 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

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)71,2404
Polymers71,0502
Non-polymers1902
Water6,413356
1
A: Nucleoside diphosphate-linked moiety X motif 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6202
Polymers35,5251
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoside diphosphate-linked moiety X motif 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6202
Polymers35,5251
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.213, 46.871, 119.606
Angle α, β, γ (deg.)90.00, 93.92, 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.4M sodium phosphate monobasic, 0.8M potassium phosphate dibasic, pH 6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.8→48.98 Å / Num. obs: 53860 / % possible obs: 99.8 % / Redundancy: 4.17 % / Net I/σ(I): 19.96
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.19 % / Mean I/σ(I) obs: 2.01 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.8→48.983 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 2693 5 %
Rwork0.199 --
obs0.2011 53860 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→48.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4461 0 10 356 4827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074575
X-RAY DIFFRACTIONf_angle_d1.1096244
X-RAY DIFFRACTIONf_dihedral_angle_d16.0591660
X-RAY DIFFRACTIONf_chiral_restr0.205699
X-RAY DIFFRACTIONf_plane_restr0.005826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7996-1.83230.34611350.30642560X-RAY DIFFRACTION98
1.8323-1.86760.30011420.28762686X-RAY DIFFRACTION100
1.8676-1.90570.29631400.28292665X-RAY DIFFRACTION100
1.9057-1.94710.3311440.26332733X-RAY DIFFRACTION100
1.9471-1.99240.3321360.25332619X-RAY DIFFRACTION100
1.9924-2.04220.25791420.24032692X-RAY DIFFRACTION100
2.0422-2.09750.28951410.23292681X-RAY DIFFRACTION100
2.0975-2.15920.28351410.22612673X-RAY DIFFRACTION100
2.1592-2.22890.28381420.2272704X-RAY DIFFRACTION100
2.2289-2.30850.2321410.21382676X-RAY DIFFRACTION100
2.3085-2.4010.24451410.21522682X-RAY DIFFRACTION100
2.401-2.51020.26871420.20862699X-RAY DIFFRACTION100
2.5102-2.64260.28221420.22681X-RAY DIFFRACTION100
2.6426-2.80810.23211420.20572717X-RAY DIFFRACTION100
2.8081-3.02490.26261420.2042692X-RAY DIFFRACTION100
3.0249-3.32920.24561440.19762728X-RAY DIFFRACTION100
3.3292-3.81080.20961430.17542714X-RAY DIFFRACTION100
3.8108-4.80060.17471440.14982742X-RAY DIFFRACTION100
4.8006-49.00090.2411490.18822823X-RAY DIFFRACTION100

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