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- PDB-4hvy: A thermostable variant of human NUDT18 NUDIX domain obtained by H... -

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Basic information

Entry
Database: PDB / ID: 4hvy
TitleA thermostable variant of human NUDT18 NUDIX domain obtained by Hot Colony Filtration
ComponentsNucleoside diphosphate-linked moiety X motif 18
KeywordsHYDROLASE / thermostability / directed evolution / Hot-CoFi / Hot Colony Filtration
Function / homology
Function and homology information


8-hydroxy-dADP phosphatase activity / dADP catabolic process / GDP catabolic process / dGDP catabolic process / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / Phosphate bond hydrolysis by NUDT proteins / magnesium ion binding / cytosol
Similarity search - Function
NUDT18, NUDIX hydrolase domain / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...NUDT18, NUDIX hydrolase domain / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
8-oxo-dGDP phosphatase NUDT18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsAsial, I. / Cheng, Y.X. / Engman, H. / Wu, B. / Dollhopf, M. / Nordlund, P. / Cornvik, T.
CitationJournal: Nat Commun / Year: 2013
Title: Engineering protein thermostability using a generic activity-independent biophysical screen inside the cell.
Authors: Asial, I. / Cheng, Y.X. / Engman, H. / Dollhopf, M. / Wu, B. / Nordlund, P. / Cornvik, T.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,76111
Polymers18,3161
Non-polymers44510
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nucleoside diphosphate-linked moiety X motif 18
hetero molecules

A: Nucleoside diphosphate-linked moiety X motif 18
hetero molecules

A: Nucleoside diphosphate-linked moiety X motif 18
hetero molecules

A: Nucleoside diphosphate-linked moiety X motif 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,04544
Polymers73,2644
Non-polymers1,78140
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area12390 Å2
ΔGint-275 kcal/mol
Surface area22140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.200, 90.200, 75.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nucleoside diphosphate-linked moiety X motif 18 / Nudix motif 18


Mass: 18316.047 Da / Num. of mol.: 1 / Fragment: NUDIX hydrolase domain containing residues 26-179 / Mutation: V45M, E91V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT18 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: Q6ZVK8, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Non-polymers , 5 types, 180 molecules

#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M tri-sodium citrate, 3.2M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2010 / Details: Rh Coated
RadiationMonochromator: Si 111 CHANNEL. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→32.34 Å / Num. all: 30904 / Num. obs: 26714 / % possible obs: 98.66 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.46 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.4-1.54150.59
1.54-1.631100
1.63-1.751100
1.75-1.881100
1.88-2.061100
2.06-2.311100
2.31-2.671100
2.67-3.26199.21
3.26-4.62185.19
4.62-32.34168.25

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→28.524 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2105 1341 5.03 %Random
Rwork0.1663 ---
obs0.1685 26681 98.37 %-
all-26714 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→28.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 24 170 1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071239
X-RAY DIFFRACTIONf_angle_d1.1471723
X-RAY DIFFRACTIONf_dihedral_angle_d12.43494
X-RAY DIFFRACTIONf_chiral_restr0.075200
X-RAY DIFFRACTIONf_plane_restr0.005222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.51220.30611410.26482536X-RAY DIFFRACTION100
1.5122-1.57270.24721330.2052533X-RAY DIFFRACTION100
1.5727-1.64430.20781110.18542555X-RAY DIFFRACTION100
1.6443-1.7310.23621410.17432527X-RAY DIFFRACTION100
1.731-1.83940.21591290.15452548X-RAY DIFFRACTION100
1.8394-1.98140.22551410.15012543X-RAY DIFFRACTION100
1.9814-2.18080.20561640.13422547X-RAY DIFFRACTION100
2.1808-2.49620.20191330.14442588X-RAY DIFFRACTION100
2.4962-3.14430.21521330.17372603X-RAY DIFFRACTION100
3.1443-28.52920.19851150.17342360X-RAY DIFFRACTION86

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