7X4Z | pdb_00007x4z

Crystal structure of Rhodostomin ARGDWP mutant

PDB DOI: https://doi.org/10.2210/pdb7X4Z/pdb

Classification: BLOOD CLOTTING
Organism(s): Calloselasma rhodostoma
Expression System: Pichia
Mutation(s): Yes

Deposited: 2022-03-03 Released: 2023-03-08
Deposition Author(s): Chang, Y.T., Chuang, W.J.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.214 (Depositor), 0.230 (DCC)
R-Value Work:
0.163 (Depositor), 0.170 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Rhodostomin ARGDWP mutant

Chang, Y.T., Chuang, W.J.

To be published.

Macromolecule Content

Total Structure Weight: 15.03 kDa
Atom Count: 1,130
Modeled Residue Count: 132
Deposited Residue Count: 136
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disintegrin rhodostomin	A, B	68	Calloselasma rhodostoma	Mutation(s): 2
UniProt
Find proteins for P30403 (Calloselasma rhodostoma) Explore P30403 Go to UniProtKB: P30403
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30403
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B], D [auth B], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.214 (Depositor), 0.230 (DCC)
R-Value Work: 0.163 (Depositor), 0.170 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.709	α = 90
b = 79.281	β = 90
c = 92.011	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History (Full details and data files)

Version 1.0: 2023-03-08
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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.