6JMS | pdb_00006jms

CJP38, a beta-1,3-glucanase and allergen of Cryptomeria japonica pollen

PDB DOI: https://doi.org/10.2210/pdb6JMS/pdb

Classification: HYDROLASE
Organism(s): Cryptomeria japonica
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-13 Released: 2020-05-06
Deposition Author(s): Takashima, T., Numata, T., Fukamizo, T., Ohnuma, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.168 (Depositor), 0.171 (DCC)
R-Value Work:
0.148 (Depositor), 0.150 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6JMS

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

Literature

CJP38, a beta-1,3-glucanase and allergen of Cryptomeria japonica pollen

Takashima, T., Fukamizo, T., Ohnuma, T., Numata, T.

To be published.

Macromolecule Content

Total Structure Weight: 35.9 kDa
Atom Count: 2,871
Modeled Residue Count: 320
Deposited Residue Count: 327
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pollen allergen CJP38	A	327	Cryptomeria japonica	Mutation(s): 0 EC: 3.2.1.39
UniProt
Find proteins for Q588B8 (Cryptomeria japonica) Explore Q588B8 Go to UniProtKB: Q588B8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q588B8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		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: 1.50 Å
R-Value Free: 0.168 (Depositor), 0.171 (DCC)
R-Value Work: 0.148 (Depositor), 0.150 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.423	α = 90
b = 71.423	β = 90
c = 63.447	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-05-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-05-06
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.