1J4G | pdb_00001j4g

crystal structure analysis of the trichosanthin delta C7

PDB DOI: https://doi.org/10.2210/pdb1J4G/pdb

Classification: HYDROLASE
Organism(s): Trichosanthes kirilowii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2001-09-30 Released: 2001-10-24
Deposition Author(s): Ding, Y., Too, H.M., Wang, Z.L., Liu, Y.W., Dong, Y.C., Shaw, P.C., Rao, Z.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.235 (Depositor)
R-Value Work:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1J4G

This is version 1.4 of the entry. See complete history.

Literature

crystal structure analysis of the trichosanthin delta C7

Ding, Y., Too, H.M., Wang, Z.L., Liu, Y.W., Dong, Y.C., Shaw, P.C., Rao, Z.H.

To be published.

Macromolecule Content

Total Structure Weight: 109.35 kDa
Atom Count: 8,483
Modeled Residue Count: 964
Deposited Residue Count: 992
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trichosanthin delta C7	A, B, C, D	248	Trichosanthes kirilowii	Mutation(s): 0 EC: 3.2.2.22
UniProt
Find proteins for P09989 (Trichosanthes kirilowii) Explore P09989 Go to UniProtKB: P09989
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09989
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain H [auth D] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.235 (Depositor)
R-Value Work: 0.174 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.56	α = 90
b = 74.4	β = 96.96
c = 87.56	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2001-10-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-10-24
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2022-12-21
Changes: Database references, Derived calculations
Version 1.4: 2024-05-29
Changes: Data collection

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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.