9CBE

Structure of a type III antifreeze protein isoform HPLC12 re-refined using standard protocols

PDB DOI: https://doi.org/10.2210/pdb9CBE/pdb

Classification: ANTIFREEZE PROTEIN
Organism(s): Zoarces americanus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-06-19 Released: 2024-07-17
Deposition Author(s): Wlodawer, A., Dauter, Z.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.189 (Depositor), 0.200 (DCC)
R-Value Work:
0.150 (Depositor), 0.160 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2MSI

Literature

In some cases more complicated approaches to refinement of macromolecular structures are not necessary.

Dauter, Z., Wlodawer, A.

(2024) IUCrJ 11: 643-644

PubMed: 38958017 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2052252524005803
Primary Citation of Related Structures:
9CBE

PubMed Abstract:
The manuscript `Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber' presents a novel protein structure refinement method claimed to offer improvements over traditional techniques like Refmac5 and Phenix. Our re-evaluation suggests that while the new method provides improvements, traditional methods achieve comparable results with less computational effort.

Organizational Affiliation

Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA.

Macromolecule Content

Total Structure Weight: 7.1 kDa
Atom Count: 534
Modelled Residue Count: 66
Deposited Residue Count: 66
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type-3 ice-structuring protein HPLC 12	A	66	Zoarces americanus	Mutation(s): 1
UniProt
Find proteins for P19614 (Zoarces americanus) Explore P19614 Go to UniProtKB: P19614
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19614
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.189 (Depositor), 0.200 (DCC)
R-Value Work: 0.150 (Depositor), 0.160 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.27	α = 90
b = 39.89	β = 90
c = 44.54	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-07-17
Type: Initial release

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.