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), 0.218 (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

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| 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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.203 (Depositor), 0.218 (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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-13

Deposition Author(s):

Meng, W.

Feng, T.

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

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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.