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- PDB-6l4g: Crystal structure of human NDRG3 I171M/S176H mutant -

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Basic information

Entry
Database: PDB / ID: 6l4g
TitleCrystal structure of human NDRG3 I171M/S176H mutant
ComponentsProtein NDRG3
KeywordsSIGNALING PROTEIN / alpha/beta-hydrolase fold / NDRG3 / Unfolded helix
Function / homology
Function and homology information


negative regulation of cell growth / spermatogenesis / cell differentiation / signal transduction / extracellular exosome / cytoplasm
Similarity search - Function
NDRG / Ndr family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.304 Å
AuthorsKim, K.R. / Han, B.W.
CitationJournal: Biomolecules / Year: 2020
Title: Structural and Biophysical Analyses of Human N-Myc Downstream-Regulated Gene 3 (NDRG3) Protein.
Authors: Kim, K.R. / Kim, K.A. / Park, J.S. / Jang, J.Y. / Choi, Y. / Lee, H.H. / Lee, D.C. / Park, K.C. / Yeom, Y.I. / Kim, H.J. / Han, B.W.
History
DepositionOct 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Data collection / Category: pdbx_reflns_twin / Item: _pdbx_reflns_twin.diffrn_id
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: Protein NDRG3
B: Protein NDRG3


Theoretical massNumber of molelcules
Total (without water)83,0372
Polymers83,0372
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint5 kcal/mol
Surface area24850 Å2
Unit cell
Length a, b, c (Å)100.387, 100.387, 111.756
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein NDRG3 / N-myc downstream-regulated gene 3 protein


Mass: 41518.688 Da / Num. of mol.: 2 / Mutation: I171M, S176H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDRG3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGV2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200 mM ammonium citrate tribasic pH 7.0 and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.4992
pseudo-merohedral21-K, -H, -L20.5008
ReflectionResolution: 3.3→50 Å / Num. obs: 10073 / % possible obs: 99.3 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 14
Reflection shellResolution: 3.3→3.36 Å / Rmerge(I) obs: 0.629 / Num. unique obs: 485

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L4B

6l4b


Resolution: 3.304→47.006 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.868 / Cross valid method: FREE R-VALUE / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2263 438 4.792 %
Rwork0.1961 --
all0.198 --
obs-9141 90.05 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.22 Å2
Baniso -1Baniso -2Baniso -3
1--8.694 Å2-0 Å2-0 Å2
2---8.694 Å2-0 Å2
3---17.389 Å2
Refinement stepCycle: LAST / Resolution: 3.304→47.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4344 0 0 6 4350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134437
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174040
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.6356033
X-RAY DIFFRACTIONr_angle_other_deg2.3191.5679424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.96824.381226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69115733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3861516
X-RAY DIFFRACTIONr_chiral_restr0.0470.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024980
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02832
X-RAY DIFFRACTIONr_nbd_refined0.2140.21084
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2230.24163
X-RAY DIFFRACTIONr_nbtor_refined0.1510.22166
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0640.21755
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.298
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2780.218
X-RAY DIFFRACTIONr_nbd_other0.330.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.22
X-RAY DIFFRACTIONr_mcbond_it1.8283.612236
X-RAY DIFFRACTIONr_mcbond_other1.8273.6092235
X-RAY DIFFRACTIONr_mcangle_it3.2825.42788
X-RAY DIFFRACTIONr_mcangle_other3.2815.4022789
X-RAY DIFFRACTIONr_scbond_it1.2263.6942201
X-RAY DIFFRACTIONr_scbond_other1.2263.6942201
X-RAY DIFFRACTIONr_scangle_it2.3055.4993245
X-RAY DIFFRACTIONr_scangle_other2.3055.53246
X-RAY DIFFRACTIONr_lrange_it5.48743.5144922
X-RAY DIFFRACTIONr_lrange_other5.48743.5264923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.304-3.3890.226170.23352X-RAY DIFFRACTION49.4638
3.389-3.4810.328290.222402X-RAY DIFFRACTION59.4483
3.481-3.5820.21240.235491X-RAY DIFFRACTION73.9943
3.582-3.6920.34260.2539X-RAY DIFFRACTION84.4544
3.692-3.8120.264310.204571X-RAY DIFFRACTION94.2097
3.812-3.9450.336260.25623X-RAY DIFFRACTION99.2355
3.945-4.0930.185370.212560X-RAY DIFFRACTION100
4.093-4.2590.386170.186582X-RAY DIFFRACTION100
4.259-4.4470.182220.17547X-RAY DIFFRACTION99.6497
4.447-4.6620.167220.139522X-RAY DIFFRACTION99.8165
4.662-4.9120.098180.149506X-RAY DIFFRACTION100
4.912-5.2060.212350.164465X-RAY DIFFRACTION100
5.206-5.5620.177160.174459X-RAY DIFFRACTION100
5.562-6.0010.227220.21411X-RAY DIFFRACTION100
6.001-6.5640.171200.222384X-RAY DIFFRACTION99.5074
6.564-7.3230.225130.195352X-RAY DIFFRACTION100
7.323-8.4260.186140.191318X-RAY DIFFRACTION100
8.426-10.2480.208230.154273X-RAY DIFFRACTION100
10.248-14.1970.217160.164208X-RAY DIFFRACTION97.3913
14.197-47.0060.248100.368138X-RAY DIFFRACTION99.3289

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