9K7W | pdb_00009k7w

Crystal structure of designed nickel-induced homotrimer C3-Ni1-HH*3-18

PDB DOI: https://doi.org/10.2210/pdb9K7W/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-24 Released: 2025-10-29
Deposition Author(s): Qu, Y.N., Cao, L.X.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.293 (Depositor), 0.293 (DCC)
R-Value Work:
0.216 (Depositor), 0.216 (DCC)
R-Value Observed:
0.220 (Depositor)

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

Validation slider image for 9K7W

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

Literature

De novo design of metal ion regulated protein assemblies

Qu, Y.N., Cao, L.X.

To be published.

Macromolecule Content

Total Structure Weight: 75.7 kDa
Atom Count: 4,627
Modeled Residue Count: 533
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C3-Ni1-HH*3-18	A, B, C, D, E A, B, C, D, E, F	112	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain K [auth E] SDF format, chain I [auth C] SDF format, chain H [auth B] MOL2 format, chain L [auth F] MOL2 format, chain K [auth E] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] mmCIF format, chain L [auth F] mmCIF format, chain K [auth E] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B]	H [auth B], I [auth C], K [auth E], L [auth F]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth E] Focus chain L [auth F]
NI (Subject of Investigation/LOI) Query on NI Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain G [auth A] MOL2 format, chain J [auth D] MOL2 format, chain G [auth A] mmCIF format, chain J [auth D] mmCIF format, chain G [auth A]	G [auth A], J [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.293 (Depositor), 0.293 (DCC)
R-Value Work: 0.216 (Depositor), 0.216 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.464	α = 90
b = 77.921	β = 95.26
c = 68.417	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-10-29
Type: Initial release

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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.