PDB-6l4h: Crystal structure of human NDRG3 C30S mutant

ID or keywords:

Entry

Database: PDB / ID: 6l4h

Title

Crystal structure of human NDRG3 C30S 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: 3.4 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	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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6l4h.cif.gz	413.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6l4h.ent.gz	339.8 KB	Display	PDB format
PDBx/mmJSON format	6l4h.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l4/6l4h ftp://data.pdbj.org/pub/pdb/validation_reports/l4/6l4h	HTTPS FTP

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Related structure data

Related structure data	6l4bSC 6l4gC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6l4b-2 4nhy-3 6l4b-1 3mgu-d 6for-1 5cux-d 3ek6-2 2r1k-2 4xd6-d 5u0w-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

C: Protein NDRG3

D: Protein NDRG3

166 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein NDRG3

B: Protein NDRG3

defined by author
Evidence: gel filtration
82.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Protein NDRG3

D: Protein NDRG3

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

Unit cell

Length a, b, c (Å)	99.759, 99.759, 332.710
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Protein NDRG3 / N-myc downstream-regulated gene 3 protein Mass: 41433.520 Da / Num. of mol.: 4 / Mutation: C30S 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

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.35 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 200 mM sodium citrate tribasic dehydrate, 20% PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å

Detector

Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 4, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 3.4→50 Å / Num. obs: 26798 / % possible obs: 97.7 % / Redundancy: 6.6 % / R_merge(I) obs: 0.103 / R_pim(I) all: 0.039 / R_rim(I) all: 0.111 / Χ²: 0.965 / Net I/σ(I): 6.4 / Num. measured all: 177018

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
3.4-3.46	6.7	0.732	1311	0.826	0.275	0.787	0.975	97.5
3.46-3.52	6.9	0.58	1296	0.864	0.216	0.623	1.023	97.5
3.52-3.59	6.8	0.494	1316	0.908	0.185	0.531	1.067	98
3.59-3.66	6.8	0.357	1318	0.921	0.135	0.384	1.069	98
3.66-3.74	6.7	0.324	1310	0.925	0.123	0.349	1.096	97.8
3.74-3.83	6.6	0.315	1343	0.943	0.12	0.339	1.041	97.5
3.83-3.92	6.7	0.271	1291	0.96	0.102	0.291	1.032	97.7
3.92-4.03	6.6	0.244	1324	0.969	0.092	0.263	1.008	97.4
4.03-4.15	6.4	0.202	1327	0.978	0.077	0.218	1.006	97.9
4.15-4.28	6.6	0.189	1296	0.983	0.072	0.204	1.058	97.6
4.28-4.44	6.4	0.126	1322	0.991	0.049	0.136	1.023	97.7
4.44-4.61	6.5	0.111	1348	0.992	0.042	0.12	0.949	97.3
4.61-4.82	6.3	0.095	1316	0.994	0.037	0.102	0.917	97.2
4.82-5.08	6.3	0.084	1343	0.995	0.033	0.091	0.868	97.5
5.08-5.4	6.3	0.083	1324	0.994	0.032	0.09	0.835	96.6
5.4-5.81	6.3	0.073	1339	0.996	0.028	0.079	0.805	96.9
5.81-6.4	6.2	0.074	1339	0.995	0.028	0.08	0.776	96.9
6.4-7.32	6.2	0.06	1383	0.996	0.023	0.064	0.732	97.9
7.32-9.21	6.4	0.042	1433	0.998	0.017	0.046	0.81	99.9
9.21-50	8.1	0.043	1519	0.998	0.015	0.045	1.101	98.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6L4B

6l4b

Resolution: 3.4→47.824 Å / Cor.coef. F_o:F_c: 0.873 / Cor.coef. F_o:F_c free: 0.831 / WR_factor R_free: 0.252 / WR_factor R_work: 0.222 / SU B: 69.859 / SU ML: 0.464 / Average fsc free: 0.9008 / Average fsc work: 0.9081 / Cross valid method: THROUGHOUT / ESU R Free: 0.568
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2774	1332	5.013 %	RANDOM
R_work	0.2415	25238	-	-
all	0.243	-	-	-
obs	-	26570	96.992 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 121.104 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.134 Å²	-0.567 Å²	-0 Å²
2-	-	-1.134 Å²	0 Å²
3-	-	-	3.678 Å²

Refinement step

Cycle: LAST / Resolution: 3.4→47.824 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8670	0	0	0	8670

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.013	8855
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	8083
X-RAY DIFFRACTION	r_angle_refined_deg	1.246	1.635	12041
X-RAY DIFFRACTION	r_angle_other_deg	2.296	1.567	18851
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.677	5	1110
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.621	24.368	451
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.709	15	1464
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.419	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.046	0.2	1166
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	9942
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1662
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	2026
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.226	0.2	7904
X-RAY DIFFRACTION	r_nbtor_refined	0.154	0.2	4251
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.063	0.2	3608
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	123
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.175	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.248	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.221	0.2	40
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.284	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.906	7.732	4461
X-RAY DIFFRACTION	r_mcbond_other	1.906	7.731	4460
X-RAY DIFFRACTION	r_mcangle_it	3.433	11.591	5564
X-RAY DIFFRACTION	r_mcangle_other	3.433	11.593	5565
X-RAY DIFFRACTION	r_scbond_it	1.627	7.837	4394
X-RAY DIFFRACTION	r_scbond_other	1.627	7.838	4395
X-RAY DIFFRACTION	r_scangle_it	2.866	11.69	6477
X-RAY DIFFRACTION	r_scangle_other	2.866	11.691	6478
X-RAY DIFFRACTION	r_lrange_it	4.888	90.967	9530
X-RAY DIFFRACTION	r_lrange_other	4.888	90.978	9531

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 (%)
3.4-3.488	0.311	88	0.312	1701	X-RAY DIFFRACTION	91.229
3.488-3.583	0.314	86	0.308	1779	X-RAY DIFFRACTION	95.7392
3.583-3.686	0.299	97	0.289	1734	X-RAY DIFFRACTION	97.4454
3.686-3.799	0.317	77	0.278	1687	X-RAY DIFFRACTION	97.7827
3.799-3.923	0.317	98	0.259	1636	X-RAY DIFFRACTION	97.5253
3.923-4.06	0.271	88	0.249	1566	X-RAY DIFFRACTION	97.4087
4.06-4.212	0.315	89	0.246	1554	X-RAY DIFFRACTION	97.6233
4.212-4.383	0.282	78	0.21	1480	X-RAY DIFFRACTION	97.9258
4.383-4.576	0.238	80	0.196	1424	X-RAY DIFFRACTION	97.0949
4.576-4.797	0.203	88	0.199	1365	X-RAY DIFFRACTION	97.3208
4.797-5.054	0.233	67	0.197	1298	X-RAY DIFFRACTION	97.5697
5.054-5.357	0.241	60	0.209	1223	X-RAY DIFFRACTION	96.5387
5.357-5.723	0.255	58	0.213	1171	X-RAY DIFFRACTION	97.0008
5.723-6.174	0.313	59	0.224	1105	X-RAY DIFFRACTION	97.0809
6.174-6.753	0.267	48	0.244	1002	X-RAY DIFFRACTION	96.9529
6.753-7.533	0.27	45	0.238	953	X-RAY DIFFRACTION	98.6166
7.533-8.666	0.274	45	0.211	848	X-RAY DIFFRACTION	99.8881
8.666-10.535	0.245	32	0.206	739	X-RAY DIFFRACTION	99.8705
10.535-14.579	0.291	34	0.245	601	X-RAY DIFFRACTION	99.686
14.579-47.824	0.406	15	0.423	372	X-RAY DIFFRACTION	95.5556

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.8726	-1.0593	-0.6615	1.5377	0.1831	0.4454	0.1664	-0.0518	0.0809	-0.19	-0.0576	-0.0895	-0.0203	0.0286	-0.1088	0.8222	-0.0576	0.0541	0.3546	0.2774	0.4523	25.783	-24.4557	-53.1431
2	2.0372	0.9341	0.8847	1.6037	0.4922	0.9789	0.2054	-0.0457	0.0615	0.0195	-0.0914	0.093	-0.0539	-0.0052	-0.114	0.7854	-0.0059	-0.0566	0.3693	0.2254	0.4897	-10.4921	-26.4076	-48.5784
3	0.7975	0.0419	0.7451	1.1543	-0.6119	1.6427	0.4252	0.0001	-0.0421	0.1767	-0.3367	-0.1579	0.0924	-0.052	-0.0885	1.0885	-0.4415	-0.4244	0.5129	0.3806	0.3022	17.0444	-39.9732	-16.4747
4	0.5117	0.2709	0.2802	2.679	-0.5572	0.9368	0.1141	-0.0288	0.0342	-0.0815	0.2319	0.057	0.2736	-0.2356	-0.346	1.0805	-0.752	-0.6307	0.5408	0.4621	0.4981	-5.459	-69.3376	-12.7358

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	29 - 317
2	X-RAY DIFFRACTION	2	ALL	B	29 - 317
3	X-RAY DIFFRACTION	3	ALL	C	29 - 317
4	X-RAY DIFFRACTION	4	ALL	D	29 - 317

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