3GE4 | pdb_00003ge4

Crystal structure of ferritin:DNA-binding protein DPS from Brucella Melitensis

PDB DOI: https://doi.org/10.2210/pdb3GE4/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Brucella melitensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-25 Released: 2009-03-03
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.179 (Depositor), 0.190 (DCC)
R-Value Work:
0.143 (Depositor), 0.150 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of ferritin:DNA-binding protein DPS from Brucella Melitensis

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 232.2 kDa
Atom Count: 17,437
Modeled Residue Count: 1,932
Deposited Residue Count: 2,076
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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	173	Brucella melitensis	Mutation(s): 0 Gene Names: BMEI1980
UniProt
Find proteins for Q8YE98 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YE98 Go to UniProtKB: Q8YE98
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8YE98
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain X [auth L] SDF format, chain W [auth K] SDF format, chain V [auth J] SDF format, chain U [auth I] SDF format, chain T [auth H] SDF format, chain S [auth G] SDF format, chain R [auth F] SDF format, chain Q [auth E] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain N [auth B] SDF format, chain M [auth A] MOL2 format, chain X [auth L] MOL2 format, chain W [auth K] MOL2 format, chain V [auth J] MOL2 format, chain U [auth I] MOL2 format, chain T [auth H] MOL2 format, chain S [auth G] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] mmCIF format, chain X [auth L] mmCIF format, chain W [auth K] mmCIF format, chain V [auth J] mmCIF format, chain U [auth I] mmCIF format, chain T [auth H] mmCIF format, chain S [auth G] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth E] M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.179 (Depositor), 0.190 (DCC)
R-Value Work: 0.143 (Depositor), 0.150 (DCC)
R-Value Observed: 0.145 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33GE4

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.24	α = 90
b = 98.33	β = 89.98
c = 105.45	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-03-03

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2009-03-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description