6LKP | pdb_00006lkp

Crystal structure of Dps1 from the thermophilic non-heterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O-77

PDB DOI: https://doi.org/10.2210/pdb6LKP/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Leptolyngbya sp. O-77
Mutation(s): No

Deposited: 2019-12-19 Released: 2020-03-25
Deposition Author(s): Minato, T., Teramoto, T., Kakuta, Y., Ogo, S., Yoon, K.S.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.315 (Depositor), 0.313 (DCC)
R-Value Work:
0.253 (Depositor), 0.254 (DCC)
R-Value Observed:
0.257 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Biochemical and structural characterization of a thermostable Dps protein with His-type ferroxidase centers and outer metal-binding sites.

Minato, T., Teramoto, T., Kakuta, Y., Ogo, S., Yoon, K.S.

(2020) FEBS Open Bio 10: 1219-1229

PubMed: 32170832 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/2211-5463.12837
Primary Citation Related Structures:
6LKP

PubMed Abstract:
The DNA-binding protein from starved cells (Dps) is found in a wide range of microorganisms, and it has been well characterized. However, little is known about Dps proteins from nonheterocystous filamentous cyanobacteria. In this study, a Dps protein from the thermophilic nonheterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O-77 (TlDps1) was purified and characterized. PAGE and CD analyses of TlDps1 demonstrated that it had higher thermostability than previously reported Dps proteins. X-ray crystallographic analysis revealed that TlDps1 possessed His-type ferroxidase centers within the cavity and unique metal-binding sites located on the surface of the protein, which presumably contributed to its exceedingly high thermostability.

Organizational Affiliation

Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan.

Macromolecule Content

Total Structure Weight: 125.48 kDa
Atom Count: 7,992
Modeled Residue Count: 1,001
Deposited Residue Count: 1,104
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA protection during starvation protein	A, B, C, D, E A, B, C, D, E, F	184	Leptolyngbya sp. O-77	Mutation(s): 0 EC: 1.16

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain X [auth D] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain L [auth B] SDF format, chain K [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain BA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth F]	BA [auth F] G [auth A] H [auth A] K [auth A] L [auth B] BA [auth F], G [auth A], H [auth A], K [auth A], L [auth B], O [auth B], P [auth B], S [auth C], T [auth D], U [auth D], X [auth D], Y [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth D] Focus chain Y [auth E]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain DA [auth F] SDF format, chain CA [auth F] SDF format, chain AA [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] CA [auth F] DA [auth F] I [auth A] J [auth A] AA [auth E], CA [auth F], DA [auth F], I [auth A], J [auth A], M [auth B], N [auth B], Q [auth C], R [auth C], V [auth D], W [auth D], Z [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.315 (Depositor), 0.313 (DCC)
R-Value Work: 0.253 (Depositor), 0.254 (DCC)
R-Value Observed: 0.257 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.787	α = 90
b = 92.787	β = 90
c = 261.12	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JPMJCR18R2

Revision History (Full details and data files)

Version 1.0: 2020-03-25
Type: Initial release
Version 2.0: 2020-04-01
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2020-09-30
Changes: Database references, Derived calculations
Version 2.2: 2023-11-22
Changes: Data collection, Database references, Refinement description