6JCC | pdb_00006jcc

structure of a de novo protein D_1CY5_M1

PDB DOI: https://doi.org/10.2210/pdb6JCC/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
Mutation(s): No

Deposited: 2019-01-28 Released: 2019-03-13
Deposition Author(s): Meng, W., Feng, T.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.203 (Depositor), 0.220 (DCC)
R-Value Work:
0.186 (Depositor), 0.210 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

structure of a computationally designed mutant protein D_1CY5_M1

Meng, W., Haiyan, L.

To be published.

Macromolecule Content

Total Structure Weight: 11.09 kDa
Atom Count: 841
Modeled Residue Count: 97
Deposited Residue Count: 97
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Computational designed protein based on evolution	A	97	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.203 (Depositor), 0.220 (DCC)
R-Value Work: 0.186 (Depositor), 0.210 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.321	α = 90
b = 38.159	β = 90
c = 64.153	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-03-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31370755

Revision History (Full details and data files)

Version 1.0: 2019-03-13
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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.