PDB-3qkp: Protein Tyrosine Phosphatase 1B - Apo W179F mutant with open WPD-loop

ID or keywords:

Entry

Database: PDB / ID: 3qkp

Title

Protein Tyrosine Phosphatase 1B - Apo W179F mutant with open WPD-loop

Components

Tyrosine-protein phosphatase non-receptor type 1

Keywords

HYDROLASE /

P-loop / WPD-loop /

Protein Phosphatase / EGFR receptor /

Phosphoprotein

Function / homology

Function and homology information

regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway /

regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane ...regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway /

regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway /

regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling /

regulation of signal transduction / cellular response to unfolded protein / positive regulation of protein tyrosine kinase activity / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / MECP2 regulates neuronal receptors and channels / endoplasmic reticulum unfolded protein response / Growth hormone receptor signaling / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling /

ephrin receptor binding / Integrin signaling / protein dephosphorylation / negative regulation of MAP kinase activity /

protein-tyrosine-phosphatase / protein phosphatase 2A binding /

protein tyrosine phosphatase activity / endosome lumen /

insulin receptor binding / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade /

receptor tyrosine kinase binding / insulin receptor signaling pathway / actin cytoskeleton organization /

early endosome /

mitochondrial matrix /

cadherin binding /

protein kinase binding /

enzyme binding /

endoplasmic reticulum / protein-containing complex /

RNA binding / zinc ion binding /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Brandao, T.A.S. / Johnson, S.J. / Hengge, A.C.

Citation

Journal: Arch.Biochem.Biophys. / Year: 2012
Title: The molecular details of WPD-loop movement differ in the protein-tyrosine phosphatases YopH and PTP1B.
Authors: Brandao, T.A. / Johnson, S.J. / Hengge, A.C.

History

Deposition	Feb 1, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 8, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3qkp.cif.gz	140.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3qkp.ent.gz	109.3 KB	Display	PDB format
PDBx/mmJSON format	3qkp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qk/3qkp ftp://data.pdbj.org/pub/pdb/validation_reports/qk/3qkp	HTTPS FTP

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Related structure data

Related structure data	3qkqC 2cm2S 3f99 3qkn PDB Unreleased entry 3qko PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1pty-d 5qf8-d 1nny-d 6b95-d 3d9c-d 1a5y-d 6bai-d 1nl9-d 5ka2-d 6phs-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
Related items in Molecule of the Month	#126 - Jun 2010 Epidermal Growth Factor similarity (20) #194 - Feb 2016 Designer Insulins similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #128 - Aug 2010 Interferons similarity (2) #134 - Feb 2011 Integrin similarity (1) #52 - Apr 2004 Growth Hormone similarity (1) #145 - Jan 2012 Messenger RNA Capping similarity (5) #225 - Sep 2018 Phytase similarity (5) #14 - Feb 2001 Insulin similarity (1) #122 - Feb 2010 Enhanceosome similarity (3) #222 - Jun 2018 Proteins and Nanoparticles similarity (1) #83 - Nov 2006 Fibrin similarity (1) #208 - Apr 2017 Glucose Transporters similarity (1) #217 - Jan 2018 Opioid Receptors similarity (1) #209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#126 - Jun 2010
Epidermal Growth Factor
similarity (20)
#194 - Feb 2016
Designer Insulins
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#128 - Aug 2010
Interferons
similarity (2)
#134 - Feb 2011
Integrin
similarity (1)
#52 - Apr 2004
Growth Hormone
similarity (1)
#145 - Jan 2012
Messenger RNA Capping
similarity (5)
#225 - Sep 2018
Phytase
similarity (5)
#14 - Feb 2001
Insulin
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (3)
#222 - Jun 2018
Proteins and Nanoparticles
similarity (1)
#83 - Nov 2006
Fibrin
similarity (1)
#208 - Apr 2017
Glucose Transporters
similarity (1)
#217 - Jan 2018
Opioid Receptors
similarity (1)
#209 - May 2017
Tissue Transglutaminase and Celiac Disease
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)

Deposited unit

A: Tyrosine-protein phosphatase non-receptor type 1

hetero molecules

37.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	88.282, 88.282, 104.535
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Tyrosine-protein phosphatase non-receptor type 1 / Protein-tyrosine phosphatase 1B / PTP-1B Mass: 37326.605 Da / Num. of mol.: 1 / Fragment: Catalytic domain, residues 1-321 / Mutation: W179F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ptp1b, ptpn1 / Plasmid: pEt-19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#3: 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
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 239 / 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: 3.15 Å³/Da / Density % sol: 60.96 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2uL of protein solution (12 mg/mL PTP1B W179F in 10 mM Tris pH 7.5, 25 mM NaCl, 0.2 mM EDTA and 3 mM DTT), 0.5 uL sucrose 30 % (w/v) and 3 uL of precipitant solution (0.1 M Hepes pH 7.5, 0.2 ...Details: 2uL of protein solution (12 mg/mL PTP1B W179F in 10 mM Tris pH 7.5, 25 mM NaCl, 0.2 mM EDTA and 3 mM DTT), 0.5 uL sucrose 30 % (w/v) and 3 uL of precipitant solution (0.1 M Hepes pH 7.5, 0.2 M magnesium acetate and 15-20 % polyethylene glycol 8000). The well solution was 500 uL of precipitant solution., vapor diffusion, sitting drop, temperature 277K

Crystal

Density Matthews: 3.15 Å³/Da / Density % sol: 60.96 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2uL of protein solution (12 mg/mL PTP1B W179F in 10 mM Tris pH 7.5, 25 mM NaCl, 0.2 mM EDTA and 3 mM DTT), 0.5 uL sucrose 30 % (w/v) and 3 uL of precipitant solution (0.1 M Hepes pH 7.5, 0.2 ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 10, 2007 / Details: mirrors

Radiation

Monochromator: Osmic Blue Optics / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.05→50 Å / Num. all: 29808 / Num. obs: 29808 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / B_iso Wilson estimate: 29.37 Å² / R_merge(I) obs: 0.103 / Χ²: 1.215 / Net I/σ(I): 10.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.05-2.12	6.1	0.649	2888	0.991	1	97.8
2.12-2.21	6.2	0.487	2949	0.983	1	98
2.21-2.31	4.5	0.54	2881	2.679	1	97.4
2.31-2.43	6.1	0.31	2928	1.08	1	98.3
2.43-2.58	5.7	0.329	2950	1.565	1	98.8
2.58-2.78	6.2	0.185	2973	1.131	1	99
2.78-3.06	6.1	0.129	2995	1.096	1	99.4
3.06-3.51	5.9	0.1	3021	1.057	1	99.5
3.51-4.42	5.8	0.066	3054	1.033	1	99.7
4.42-50	5.9	0.034	3169	1.038	1	99.2

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.6.4_486	refinement
PDB_EXTRACT	3.1	data extraction
CrystalClear		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2CM2 with the active site water molecules removed

2cm2

Resolution: 2.05→38.227 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8196 / SU ML: 0.28 / σ(F): 0 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2452	1496	5.05 %	Random
R_work	0.204	-	-	-
all	0.2061	29632	-	-
obs	0.2061	29632	98.22 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 54.363 Å² / k_sol: 0.362 e/Å³

Displacement parameters

B_iso max: 138.06 Å² / B_iso mean: 39.0278 Å² / B_iso min: 11.71 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.0818 Å²	0 Å²	0 Å²
2-	-	0.0818 Å²	0 Å²
3-	-	-	-0.1636 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→38.227 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2372	0	20	239	2631

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2442
X-RAY DIFFRACTION	f_angle_d	1.104	3286
X-RAY DIFFRACTION	f_chiral_restr	0.078	348
X-RAY DIFFRACTION	f_plane_restr	0.004	422
X-RAY DIFFRACTION	f_dihedral_angle_d	14.158	932

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.05-2.1135	0.3534	152	0.2956	2450	2602	97
2.1135-2.1891	0.2915	130	0.2575	2536	2666	98
2.1891-2.2767	0.5289	121	0.4201	2381	2502	93
2.2767-2.3803	0.263	151	0.2594	2511	2662	98
2.3803-2.5058	0.2235	137	0.2206	2558	2695	99
2.5058-2.6627	0.2709	120	0.2005	2548	2668	99
2.6627-2.8683	0.2619	141	0.2013	2564	2705	99
2.8683-3.1568	0.2401	138	0.1921	2610	2748	100
3.1568-3.6133	0.2294	144	0.1852	2579	2723	99
3.6133-4.5512	0.2064	132	0.1613	2648	2780	99
4.5512-38.2339	0.1865	130	0.1761	2751	2881	99

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	0.1004	-0.3259	0.1984	2.3828	-0.524	2.4095	-0.2213	0.1765	0.2963	-0.3787	0.3748	0.9488	-0.1369	-0.8869	-0.1029	0.1468	0.0492	-0.1159	0.4226	0.0604	0.3949	24.5846	-12.0447	10.4011
2	0.4133	0.061	0.0595	0.1614	-0.3317	0.9848	0.0767	0.0566	0.0482	-0.3749	-0.0713	-0.2566	-0.3887	-0.0315	-0.0103	0.327	0.0642	0.0819	0.1068	0.0346	0.2544	50.6329	-2.3319	6.5717
3	0.4025	-0.0727	-0.2232	0.094	-0.1007	0.5035	0.0887	0.0639	0.3099	0.055	-0.083	-0.2385	-0.407	0.145	-0.0106	0.2216	-0.0128	-0.0221	0.0675	0.0144	0.2464	57.9622	-3.3017	14.7417
4	0.8393	-0.2586	-0.5642	1.5987	-0.0046	0.5627	0.0371	0.0472	0.1541	0.0138	-0.0329	-0.2024	-0.0014	-0.0083	-0.0032	0.1713	0.0434	-0.0044	0.1132	-0.0053	0.1412	51.3596	-16.0874	14.1392
5	1.3442	-1.1197	-0.5529	1.7596	-0.3055	1.1231	0.1174	-0.1243	0.3175	-0.1186	-0.3296	-0.0857	0.1359	0.3562	0.1316	0.1669	0.0913	0.0147	0.1826	0.0388	0.3219	65.4449	-23.5993	15.079
6	1.9638	0.3425	0.0239	0.5034	-0.0874	0.8163	-0.1134	-0.0723	-0.4555	0.0768	0.207	-0.3421	0.1369	0.0289	-0.1136	0.2081	0.0892	-0.023	0.1131	-0.0034	0.2118	56.3316	-24.9819	19.903
7	5.7272	-1.6021	-2.3155	3.8412	-1.292	6.3682	0.1356	1.4979	1.3629	0.1499	-0.3997	-0.273	0.2681	-0.9146	0.2153	0.31	-0.0181	0.1343	0.5194	0.0723	0.3832	37.7392	-26.6446	4.9073
8	0.9843	0.9333	-0.6925	2.1171	0.9408	3.4305	-0.2025	-0.1972	0.0498	0.2514	-0.0481	0.4992	0.6876	0.1274	0.2402	0.3176	0.0217	0.0466	0.0704	-0.0038	0.1634	38.3754	-27.7287	18.6201
9	0.8611	-0.3083	-0.5983	1.0775	-0.0767	0.6123	0.0228	-0.0757	0.1279	-0.0833	0.0215	0.0583	0.1815	0.0805	-0.0334	0.1932	0.036	0.0059	0.1264	-0.0163	0.136	42.3567	-17.7466	20.207
10	3.0001	0.4277	-0.7421	0.5326	0.2142	2.3076	-0.0172	0.0067	-0.0192	0.1057	-0.0978	0.0133	0.1296	-0.3587	0.1023	0.1338	-0.0057	0.0072	0.1019	-0.0314	0.0952	30.8569	-18.3298	19.2554

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 1:31)	A	1 - 31
2	X-RAY DIFFRACTION	2	(chain A and resid 32:56)	A	32 - 56
3	X-RAY DIFFRACTION	3	(chain A and resid 57:69)	A	57 - 69
4	X-RAY DIFFRACTION	4	(chain A and resid 70:127)	A	70 - 127
5	X-RAY DIFFRACTION	5	(chain A and resid 128:147)	A	128 - 147
6	X-RAY DIFFRACTION	6	(chain A and resid 148:176)	A	148 - 176
7	X-RAY DIFFRACTION	7	(chain A and resid 177:186)	A	177 - 186
8	X-RAY DIFFRACTION	8	(chain A and resid 187:198)	A	187 - 198
9	X-RAY DIFFRACTION	9	(chain A and resid 199:234)	A	199 - 234
10	X-RAY DIFFRACTION	10	(chain A and resid 235:291)	A	235 - 291

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