6KRX | pdb_00006krx

Crystal Structure of AtPTP1 at 1.7 angstrom

PDB DOI: https://doi.org/10.2210/pdb6KRX/pdb

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2019-08-22 Released: 2020-08-26
Deposition Author(s): Zhao, Y.Y., Luo, Z.P., Wang, J., Wu, J.W.
Funding Organization(s): National Science Foundation (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.174 (Depositor), 0.196 (DCC)
R-Value Work:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6KRX

This is version 1.1 of the entry. See complete history.

Literature

AtPTP1 positively mediates brassinosteroid signaling from receptor kinases to GSK3-like kinase BIN2

Zhao, Y.Y., Wang, H.J., Hu, J., Tang, J., Zhang, W.H., He, Q.Q., Deng, H.T., Luo, Z.P., Wang, J., Wang, Z.X., Wang, X.L., Wu, J.W.

To be published.

Macromolecule Content

Total Structure Weight: 38.28 kDa
Atom Count: 2,684
Modeled Residue Count: 302
Deposited Residue Count: 340
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-tyrosine-phosphatase PTP1	A	340	Arabidopsis thaliana	Mutation(s): 0 Gene Names: PTP1, At1g71860, F14O23.24 EC: 3.1.3.48
UniProt
Find proteins for O82656 (Arabidopsis thaliana) Explore O82656 Go to UniProtKB: O82656
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O82656
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.174 (Depositor), 0.196 (DCC)
R-Value Work: 0.151 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.536	α = 90
b = 38.97	β = 110.815
c = 75.525	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (China)	China	--

Revision History (Full details and data files)

Version 1.0: 2020-08-26
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.