PDB-2nlk: Crystal structure of D1 and D2 catalytic domains of human Protein...

ID or keywords:

Entry

Database: PDB / ID: 2nlk

Title

Crystal structure of D1 and D2 catalytic domains of human Protein Tyrosine Phosphatase Gamma (D1+D2 PTPRG)

Components

Protein tyrosine phosphatase, receptor type, G variant (Fragment)

Keywords

HYDROLASE / PTPRG / R-PTP gamma / Protein Tyrosine Phosphatase gamma / D3S1249 / HPTPG / RPTPG / PTPG / D1-D2 catalytic domains / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

transmembrane receptor protein tyrosine phosphatase activity / negative regulation of epithelial cell migration / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell surface receptor protein tyrosine kinase signaling pathway / neuron projection development / negative regulation of neuron projection development / signal transduction / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Filippakopoulos, P. / Gileadi, O. / Johansson, C. / Ugochukwu, E. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC)

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2009
Title: Large-scale structural analysis of the classical human protein tyrosine phosphatome.
Authors: Barr, A.J. / Ugochukwu, E. / Lee, W.H. / King, O.N. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S.

History

Deposition	Oct 20, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 21, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Aug 30, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2nlk.cif.gz	129.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2nlk.ent.gz	97.5 KB	Display	PDB format
PDBx/mmJSON format	2nlk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2nlk_validation.pdf.gz	418.2 KB	Display	wwPDB validaton report
Full document	2nlk_full_validation.pdf.gz	422.6 KB	Display
Data in XML	2nlk_validation.xml.gz	21.8 KB	Display
Data in CIF	2nlk_validation.cif.gz	31.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nl/2nlk ftp://data.pdbj.org/pub/pdb/validation_reports/nl/2nlk	HTTPS FTP

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Related structure data

Related structure data	2ahsC 2b49C 2cfvC 2cjzC 2gjtC 2h4vSC 2i75C 2jjdC 2nz6C 2oc3C 2ooqC 2p6xC 2pa5C 2qepC 3b7oC 1gwzS 1h02S 1rpmS 1yf0S 2c7sS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4dpy-d 4bpc-d 4hjq-d 2x4f-d 5nwk-1 4g8m-1 2g4d-d 4dpu-d 3rn5-1 6uzt-2 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
Related items in Molecule of the Month	#126 - Jun 2010 Epidermal Growth Factor similarity (12) #145 - Jan 2012 Messenger RNA Capping similarity (5) #225 - Sep 2018 Phytase similarity (5) #185 - May 2015 Titin similarity (1) #52 - Apr 2004 Growth Hormone similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Protein tyrosine phosphatase, receptor type, G variant (Fragment)

71.8 kDa, 1 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)	118.510, 133.996, 59.084
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Protein tyrosine phosphatase, receptor type, G variant (Fragment) Mass: 71766.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRG / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-R3 References: UniProt: Q59EE0, UniProt: P23470*PLUS, protein-tyrosine-phosphatase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Protein tyrosine phosphatase, receptor type, G variant (Fragment)

Mass: 71766.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PTPRG / Plasmid: pNIC-CH / Production host:

Escherichia coli (E. coli) / Strain (production host): Rosetta-R3
References: UniProt: Q59EE0, UniProt: P23470*PLUS, protein-tyrosine-phosphatase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.27 Å³/Da / Density % sol: 62.35 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10% PEG 10K, 100mM Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54

Detector

Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 19, 2006

Radiation

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

Radiation wavelength

Wavelength: 1.54 Å / Relative weight: 1

Reflection

Av σ(I) over netI: 5.9 / R_merge(I) obs: 0.099 / R_sym value: 0.099 / D res high: 1.743 Å / D res low: 39.936 Å / Num. obs: 37418 / % possible obs: 99.5 / Redundancy: 4.2 %

ID	Number
1	156862
2	156861

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
7.59	39.94	97.9	1	0.036	0.036	4.6
5.37	7.59	99.8	1	0.052	0.052	4.9
4.38	5.37	100	1	0.056	0.056	4.9
3.79	4.38	100	1	0.081	0.081	4.7
3.39	3.79	99.4	1	0.135	0.135	4.1
3.1	3.39	100	1	0.122	0.122	4.5
2.87	3.1	99.9	1	0.176	0.176	4.2
2.68	2.87	99.8	1	0.242	0.242	3.9
2.53	2.68	99.2	1	0.359	0.359	3.7
2.4	2.53	98.6	1	0.485	0.485	3.6
7.59	39.94	97.9	2	0.036	0.036	4.6
5.37	7.59	99.8	2	0.052	0.052	4.9
4.38	5.37	100	2	0.056	0.056	4.9
3.79	4.38	100	2	0.081	0.081	4.7
3.39	3.79	99.4	2	0.135	0.135	4.1
3.1	3.39	100	2	0.122	0.122	4.5
2.87	3.1	99.9	2	0.176	0.176	4.2
2.68	2.87	99.8	2	0.242	0.242	3.9
2.53	2.68	99.2	2	0.359	0.359	3.7
2.4	2.53	98.6	2	0.485	0.485	3.6

Reflection

Resolution: 2.4→39.936 Å / Num. all: 37606 / Num. obs: 37418 / % possible obs: 99.5 % / Redundancy: 4.2 % / R_merge(I) obs: 0.099 / R_sym value: 0.099 / Net I/σ(I): 5.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.4-2.53	3.6	0.485	1.5	19072	5313	0.485	98.6
2.53-2.68	3.7	0.359	2.1	18995	5089	0.359	99.2
2.68-2.87	3.9	0.242	3.1	18888	4800	0.242	99.8
2.87-3.1	4.2	0.176	4.2	18942	4520	0.176	99.9
3.1-3.39	4.5	0.122	5.9	18707	4151	0.122	100
3.39-3.79	4.1	0.135	4.7	15453	3755	0.135	99.4
3.79-4.38	4.7	0.081	8.9	15954	3365	0.081	100
4.38-5.37	4.9	0.056	12	14048	2890	0.056	100
5.37-7.59	4.9	0.052	12.9	10914	2249	0.052	99.8
7.59-39.94	4.6	0.036	16.2	5889	1286	0.036	97.9

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Phasing

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.5 Å	37.89 Å
Translation	2.5 Å	37.89 Å

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Processing

Software

Name	Version	Classification
SCALA		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
CrystalClear	(MSC/RIGAKU)	data collection
MOSFLM		data reduction
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRies 2H4V, 2C7S, 1RPM, 1YF0, 1H02, 1GWZ

Resolution: 2.4→39.936 Å / Cor.coef. F_o:F_c: 0.905 / Cor.coef. F_o:F_c free: 0.887 / SU B: 14.248 / SU ML: 0.177 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.274	1864	5 %	RANDOM
R_work	0.237	-	-	-
all	0.239	37639	-	-
obs	0.239	37345	99.22 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 22.159 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.32 Å²	0 Å²	0 Å²
2-	-	-0.78 Å²	0 Å²
3-	-	-	-0.54 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→39.936 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4386	0	0	150	4536

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	4493
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2970
X-RAY DIFFRACTION	r_angle_refined_deg	1.565	1.937	6106
X-RAY DIFFRACTION	r_angle_other_deg	1.06	3	7241
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.626	5	547
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.546	24.252	214
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.692	15	742
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.899	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.133	0.2	685
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4985
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	904
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	881
X-RAY DIFFRACTION	r_nbd_other	0.193	0.2	2988
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	2114
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	2282
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	188
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.123	0.2	11
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.196	0.2	35
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.103	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	0.641	1.5	2853
X-RAY DIFFRACTION	r_mcbond_other	0.132	1.5	1103
X-RAY DIFFRACTION	r_mcangle_it	1.066	2	4479
X-RAY DIFFRACTION	r_scbond_it	1.651	3	1898
X-RAY DIFFRACTION	r_scangle_it	2.469	4.5	1627

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.362	135	-
R_work	0.296	2545	-
obs	-	2680	97.6 %

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	0.9655	-1.2886	-1.8154	4.2785	0.653	4.6384	0.1218	0.1914	-0.1129	-0.6228	-0.0649	0.4043	-0.0405	-1.053	-0.0569	0.0081	0.0286	-0.0709	0.172	0.0032	0.0312	24.5389	12.3228	40.5983
2	1.4259	-0.1039	0.1241	1.7426	0.3067	1.8868	0.0299	-0.0486	0.1152	0.1716	-0.0307	-0.1072	-0.2875	-0.0377	0.0007	0.0973	0.0225	0.0036	0.0246	-0.0091	0.0768	39.3011	23.2213	65.1063
3	0.7457	-0.1012	-0.474	1.1835	0.2943	2.3689	0.016	-0.1692	-0.0236	0.2302	-0.038	-0.0626	0.1251	0.0688	0.022	0.1205	0.0202	-0.0306	0.0311	0.0099	0.0686	42.4749	5.5455	75.2521
4	0.9478	-0.1078	0.0437	1.5556	-0.3136	1.6473	0.0026	0.0666	-0.0763	-0.0043	0.0001	0.1125	0.1322	-0.2967	-0.0026	0.0619	-0.0104	0.0154	0.0546	-0.0072	0.0618	32.1541	8.5851	57.3829
5	0.5116	0.4637	0.8589	7.7992	-2.7616	6.3172	-0.046	0.0798	-0.1984	-0.0326	0.1395	0.7058	-0.0792	-0.3538	-0.0934	-0.108	-0.0172	0.0342	0.0784	-0.0461	0.1722	20.2529	-14.2696	53.2014
6	7.7096	-0.2141	-2.31	0.9045	-0.1134	1.2185	0.3094	0.9925	0.3874	-0.0667	-0.1329	-0.1111	-0.3728	0.025	-0.1765	0.0591	-0.0401	-0.0792	0.1134	0.1192	-0.0208	43.3955	-11.6163	36.1636
7	2.5963	-0.0233	0.0616	0.9323	-0.3674	0.2185	-0.0171	0.3421	0.1647	-0.026	0.0169	-0.0057	-0.0186	0.1238	0.0002	0.0718	-0.0234	-0.0131	0.0277	-0.001	0.0915	51.4892	-16.969	45.2705
8	6.1211	2.6457	0.0628	2.9952	0.5575	0.6709	-0.0183	0.2266	-0.5907	0.055	0.0652	-0.0872	0.2371	0.0278	-0.0469	0.1017	0.0382	-0.0153	-0.0103	-0.0183	0.0865	58.6819	-27.7254	48.6838
9	2.8389	0.3908	-1.3775	0.4682	-0.5643	1.0956	-0.0243	0.0115	0.0105	0.0649	0.035	-0.095	0.0614	-0.0306	-0.0107	0.1107	-0.0266	-0.0218	-0.0038	-0.007	0.0991	40.0738	-23.8242	54.191
10	1.8416	-0.5363	0.4964	3.5521	-1.1677	3.903	-0.0166	0.1367	0.1596	0.0336	-0.0044	0.3826	0.0185	-0.2509	0.021	0.0339	-0.0179	0.0039	0.02	-0.0015	0.1105	30.5478	-18.3553	48.6746

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Auth seq-ID	Label seq-ID
1	1	827 - 852	2 - 27
2	2	853 - 932	28 - 107
3	3	933 - 1015	108 - 190
4	4	1016 - 1117	191 - 292
5	5	1118 - 1153	293 - 328
6	6	1154 - 1196	329 - 371
7	7	1204 - 1248	379 - 423
8	8	1249 - 1317	424 - 492
9	9	1318 - 1377	493 - 552
10	10	1378 - 1412	553 - 587

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