5GML | pdb_00005gml

Crystal Structure of GRASP Domain of GRASP55 with N terminal extra residues

PDB DOI: https://doi.org/10.2210/pdb5GML/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-07-14 Released: 2017-07-19
Deposition Author(s): Shi, N., Shi, X., Morelli, X., Betzi, S., Huang, X.
Funding Organization(s): National Natural Science Foundation of China, Campus France

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.311 (Depositor), 0.317 (DCC)
R-Value Work:
0.261 (Depositor), 0.273 (DCC)
R-Value Observed:
0.264 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Structural relationship of the tandem PDZ tandem from Grasp55 and its implication in the unconventional secretion pathway

Cartier-Michaud, A., Betzi, S., Shi, X., Shi, N., Morelli, X., Aurrand-Lions, M.

To be published.

Macromolecule Content

Total Structure Weight: 51.89 kDa
Atom Count: 3,499
Modeled Residue Count: 446
Deposited Residue Count: 470
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Golgi reassembly-stacking protein 2	A, B	235	Mus musculus	Mutation(s): 0 Gene Names: Gorasp2, GOLPH6
UniProt
Find proteins for Q99JX3 (Mus musculus) Explore Q99JX3 Go to UniProtKB: Q99JX3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99JX3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.311 (Depositor), 0.317 (DCC)
R-Value Work: 0.261 (Depositor), 0.273 (DCC)
R-Value Observed: 0.264 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.312	α = 90
b = 132.312	β = 90
c = 221.055	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
HKL-2000	data reduction
xia2	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-07-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31370738
Campus France	France	PHC CAI YUANPEI 2013 - Project N26203WD

Revision History (Full details and data files)

Version 1.0: 2017-07-19
Type: Initial release
Version 1.1: 2017-10-18
Changes: Author supporting evidence
Version 1.2: 2023-11-08
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.