5YV7 | pdb_00005yv7

Racemic X-ray Structure of Calcicludine

PDB DOI: https://doi.org/10.2210/pdb5YV7/pdb

Classification: TOXIN
Organism(s): Dendroaspis angusticeps
Mutation(s): No

Deposited: 2017-11-24 Released: 2017-12-27
Deposition Author(s): Shuai, G., Qian, Q., Lei, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.302 (Depositor), 0.290 (DCC)
R-Value Work:
0.289 (Depositor), 0.290 (DCC)
R-Value Observed:
0.290 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Racemic X-ray Structure of Calcicludine

Shuai, G., Qian, Q., Lei, L.

To be published.

Macromolecule Content

Total Structure Weight: 7 kDa
Atom Count: 536
Modelled Residue Count: 60
Deposited Residue Count: 60
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kunitz-type serine protease inhibitor homolog calcicludine	A	60	Dendroaspis angusticeps	Mutation(s): 0
UniProt
Find proteins for P81658 (Dendroaspis angusticeps) Explore P81658 Go to UniProtKB: P81658
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P81658
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.302 (Depositor), 0.290 (DCC)
R-Value Work: 0.289 (Depositor), 0.290 (DCC)
R-Value Observed: 0.290 (Depositor)

Space Group: I 4₁/a

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.991	α = 90
b = 95.991	β = 90
c = 39.486	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data reduction
PHENIX	model building
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-12-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-12-27
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-06
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.