9CC4 | pdb_00009cc4

Crystal structure of Z4 c3ii

PDB DOI: https://doi.org/10.2210/pdb9CC4/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-20 Released: 2025-06-25
Deposition Author(s): Bera, A.K., Pyles, H., Saragovi, A., Kang, A., Baker, D.
Funding Organization(s): National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free:
0.296 (Depositor), 0.297 (DCC)
R-Value Work:
0.240 (Depositor), 0.241 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Design of defined protein-semiconductor nano complexes

Saragovi, A., Pyles, H., Bera, A.K., Baker, D.

To be published.

Macromolecule Content

Total Structure Weight: 147.71 kDa
Atom Count: 9,242
Modeled Residue Count: 1,236
Deposited Residue Count: 1,392
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Z4 c3ii	A B C D E [auth F] A, B, C, D, E [auth F], F [auth E]	232	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: 2.99 Å
R-Value Free: 0.296 (Depositor), 0.297 (DCC)
R-Value Work: 0.240 (Depositor), 0.241 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.593	α = 90
b = 68.52	β = 90.884
c = 111.752	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-06-25
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.