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

ID or keywords:

Entry

Database: PDB / ID: 6l4g

Title

Crystal structure of human NDRG3 I171M/S176H mutant

Components

Protein NDRG3

Keywords

SIGNALING 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

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.304 Å

Authors

Kim, K.R. / Han, B.W.

Citation

Journal: 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

Deposition	Oct 16, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 26, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 7, 2021	Group: Data collection / Category: pdbx_reflns_twin / Item: _pdbx_reflns_twin.diffrn_id
Revision 1.2	Nov 22, 2023	Group: 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
Revision 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6l4g.cif.gz	121.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6l4g.ent.gz	92.3 KB	Display	PDB format
PDBx/mmJSON format	6l4g.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6l4g_validation.pdf.gz	445.1 KB	Display	wwPDB validaton report
Full document	6l4g_full_validation.pdf.gz	457.1 KB	Display
Data in XML	6l4g_validation.xml.gz	21.8 KB	Display
Data in CIF	6l4g_validation.cif.gz	28.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l4/6l4g ftp://data.pdbj.org/pub/pdb/validation_reports/l4/6l4g	HTTPS FTP

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Related structure data

Related structure data	6l4bSC 6l4hC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4fek-d 4c9d-d 5gy7-d 6vnt-d 4dmo-d 6imp-d 6bq0-d 6nji-d 2odq-d 2hg1-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protein NDRG3

B: Protein NDRG3

83 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

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 number	154
Space group name H-M	P3₂21

#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 Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.17 %
Crystal grow	Temperature: 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

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 11C / Wavelength: 0.97942 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97942 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.4992
pseudo-merohedral	2	1	-K, -H, -L	2	0.5008

Reflection

Resolution: 3.3→50 Å / Num. obs: 10073 / % possible obs: 99.3 % / Redundancy: 10.5 % / R_merge(I) obs: 0.164 / Net I/σ(I): 14

Reflection shell

Resolution: 3.3→3.36 Å / R_merge(I) obs: 0.629 / Num. unique obs: 485

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6L4B

6l4b

Resolution: 3.304→47.006 Å / Cor.coef. F_o:F_c: 0.882 / Cor.coef. F_o:F_c free: 0.868 / Cross valid method: FREE R-VALUE / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2263	438	4.792 %
R_work	0.1961	-	-
all	0.198	-	-
obs	-	9141	90.05 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 33.22 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.694 Å²	-0 Å²	-0 Å²
2-	-	-8.694 Å²	-0 Å²
3-	-	-	17.389 Å²

Refinement step

Cycle: LAST / Resolution: 3.304→47.006 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4344	0	0	6	4350

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	4437
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	4040
X-RAY DIFFRACTION	r_angle_refined_deg	1.279	1.635	6033
X-RAY DIFFRACTION	r_angle_other_deg	2.319	1.567	9424
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.054	5	556
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.968	24.381	226
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.691	15	733
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.386	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.047	0.2	585
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4980
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	832
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	1084
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.223	0.2	4163
X-RAY DIFFRACTION	r_nbtor_refined	0.151	0.2	2166
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.064	0.2	1755
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.19	0.2	98
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.044	0.2	12
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.278	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.33	0.2	73
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.133	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.828	3.61	2236
X-RAY DIFFRACTION	r_mcbond_other	1.827	3.609	2235
X-RAY DIFFRACTION	r_mcangle_it	3.282	5.4	2788
X-RAY DIFFRACTION	r_mcangle_other	3.281	5.402	2789
X-RAY DIFFRACTION	r_scbond_it	1.226	3.694	2201
X-RAY DIFFRACTION	r_scbond_other	1.226	3.694	2201
X-RAY DIFFRACTION	r_scangle_it	2.305	5.499	3245
X-RAY DIFFRACTION	r_scangle_other	2.305	5.5	3246
X-RAY DIFFRACTION	r_lrange_it	5.487	43.514	4922
X-RAY DIFFRACTION	r_lrange_other	5.487	43.526	4923

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.304-3.389	0.226	17	0.23	352	X-RAY DIFFRACTION	49.4638
3.389-3.481	0.328	29	0.222	402	X-RAY DIFFRACTION	59.4483
3.481-3.582	0.21	24	0.235	491	X-RAY DIFFRACTION	73.9943
3.582-3.692	0.34	26	0.2	539	X-RAY DIFFRACTION	84.4544
3.692-3.812	0.264	31	0.204	571	X-RAY DIFFRACTION	94.2097
3.812-3.945	0.336	26	0.25	623	X-RAY DIFFRACTION	99.2355
3.945-4.093	0.185	37	0.212	560	X-RAY DIFFRACTION	100
4.093-4.259	0.386	17	0.186	582	X-RAY DIFFRACTION	100
4.259-4.447	0.182	22	0.17	547	X-RAY DIFFRACTION	99.6497
4.447-4.662	0.167	22	0.139	522	X-RAY DIFFRACTION	99.8165
4.662-4.912	0.098	18	0.149	506	X-RAY DIFFRACTION	100
4.912-5.206	0.212	35	0.164	465	X-RAY DIFFRACTION	100
5.206-5.562	0.177	16	0.174	459	X-RAY DIFFRACTION	100
5.562-6.001	0.227	22	0.21	411	X-RAY DIFFRACTION	100
6.001-6.564	0.171	20	0.222	384	X-RAY DIFFRACTION	99.5074
6.564-7.323	0.225	13	0.195	352	X-RAY DIFFRACTION	100
7.323-8.426	0.186	14	0.191	318	X-RAY DIFFRACTION	100
8.426-10.248	0.208	23	0.154	273	X-RAY DIFFRACTION	100
10.248-14.197	0.217	16	0.164	208	X-RAY DIFFRACTION	97.3913
14.197-47.006	0.248	10	0.368	138	X-RAY DIFFRACTION	99.3289

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