4DYU | pdb_00004dyu

The crystal structure of DNA starvation/stationary phase protection protein Dps from Yersinia pestis KIM 10

PDB DOI: https://doi.org/10.2210/pdb4DYU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Yersinia pestis KIM10+
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-02-29 Released: 2012-03-14
Deposition Author(s): Tan, K., Gu, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.269 (Depositor), 0.235 (DCC)
R-Value Work:
0.179 (Depositor)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of DNA starvation/stationary phase protection protein Dps from Yersinia pestis KIM 10

Tan, K., Gu, M., Kwon, K., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 232.05 kDa
Atom Count: 15,159
Modeled Residue Count: 1,860
Deposited Residue Count: 2,040
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, G, H, I, J, K, L	170	Yersinia pestis KIM10+	Mutation(s): 0 Gene Names: dps, y1677, Yersinia pestis, YPO2510, YP_2325 EC: 1.16
UniProt
Find proteins for Q7CJ65 (Yersinia pestis) Explore Q7CJ65 Go to UniProtKB: Q7CJ65
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7CJ65
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain JA [auth K] SDF format, chain HA [auth J] SDF format, chain GA [auth J] SDF format, chain DA [auth H] SDF format, chain BA [auth G] SDF format, chain AA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain JA [auth K] MOL2 format, chain HA [auth J] MOL2 format, chain GA [auth J] MOL2 format, chain DA [auth H] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain JA [auth K] mmCIF format, chain HA [auth J] mmCIF format, chain GA [auth J] mmCIF format, chain DA [auth H] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth G] DA [auth H] GA [auth J] HA [auth J] AA [auth F], BA [auth G], DA [auth H], GA [auth J], HA [auth J], JA [auth K], N [auth A], O [auth A], Q [auth B], R [auth B], U [auth D], V [auth D], Y [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth F] Focus chain BA [auth G] Focus chain DA [auth H] Focus chain GA [auth J] Focus chain HA [auth J] Focus chain JA [auth K] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth G] Focus chain DA [auth H] Focus chain GA [auth J] Focus chain HA [auth J] Focus chain JA [auth K] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain M [auth A] SDF format, chain KA [auth L] SDF format, chain IA [auth K] SDF format, chain FA [auth J] SDF format, chain EA [auth I] SDF format, chain CA [auth H] MOL2 format, chain Z [auth F] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth L] MOL2 format, chain IA [auth K] MOL2 format, chain FA [auth J] MOL2 format, chain EA [auth I] MOL2 format, chain CA [auth H] mmCIF format, chain Z [auth F] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth L] mmCIF format, chain IA [auth K] mmCIF format, chain FA [auth J] mmCIF format, chain EA [auth I] mmCIF format, chain CA [auth H]	CA [auth H] EA [auth I] FA [auth J] IA [auth K] KA [auth L] CA [auth H], EA [auth I], FA [auth J], IA [auth K], KA [auth L], M [auth A], P [auth B], S [auth C], T [auth D], W [auth E], X [auth E], Z [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth H] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain IA [auth K] Focus chain KA [auth L] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth H] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain IA [auth K] Focus chain KA [auth L] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.269 (Depositor), 0.235 (DCC)
R-Value Work: 0.179 (Depositor)
R-Value Observed: 0.184 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.414	α = 90
b = 105.102	β = 90
c = 191.834	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-03-14

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-03-14
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description