1F30

THE STRUCTURAL BASIS FOR DNA PROTECTION BY E. COLI DPS PROTEIN

PDB DOI: https://doi.org/10.2210/pdb1F30/pdb

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

Deposited: 2000-05-31 Released: 2003-06-17
Deposition Author(s): Luo, J., Liu, D., White, M.A., Fox, R.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.272
R-Value Work: 0.232
R-Value Observed: 0.232

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The Structural Basis for DNA Protection by E. coli Dps Protein

Luo, J., Liu, D., White, M.A., Fox, R.O.

To be published.

Macromolecule Content

Total Structure Weight: 226.89 kDa
Atom Count: 15,479
Modelled Residue Count: 1,872
Deposited Residue Count: 2,004
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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	167	Escherichia coli	Mutation(s): 0 Gene Names: DPS EC: 1.16
UniProt
Find proteins for P0ABT2 (Escherichia coli (strain K12)) Explore P0ABT2 Go to UniProtKB: P0ABT2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain DA [auth J] SDF format, chain V [auth E] SDF format, chain BA [auth I] SDF format, chain EA [auth J] SDF format, chain GA [auth K] SDF format, chain IA [auth L] SDF format, chain JA [auth L] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain X [auth F] MOL2 format, chain DA [auth J] MOL2 format, chain V [auth E] MOL2 format, chain BA [auth I] MOL2 format, chain EA [auth J] MOL2 format, chain GA [auth K] MOL2 format, chain IA [auth L] MOL2 format, chain JA [auth L] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain X [auth F] mmCIF format, chain DA [auth J] mmCIF format, chain V [auth E] mmCIF format, chain BA [auth I] mmCIF format, chain EA [auth J] mmCIF format, chain GA [auth K] mmCIF format, chain IA [auth L] mmCIF format, chain JA [auth L] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain X [auth F]	BA [auth I] DA [auth J] EA [auth J] GA [auth K] IA [auth L] BA [auth I], DA [auth J], EA [auth J], GA [auth K], IA [auth L], JA [auth L], N [auth A], O [auth A], R [auth C], T [auth D], V [auth E], X [auth F]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain CA [auth J] SDF format, chain FA [auth K] SDF format, chain HA [auth L] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain Y [auth G] SDF format, chain Z [auth H] MOL2 format, chain AA [auth I] MOL2 format, chain CA [auth J] MOL2 format, chain FA [auth K] MOL2 format, chain HA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain AA [auth I] mmCIF format, chain CA [auth J] mmCIF format, chain FA [auth K] mmCIF format, chain HA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth H]	AA [auth I] CA [auth J] FA [auth K] HA [auth L] M [auth A] AA [auth I], CA [auth J], FA [auth K], HA [auth L], M [auth A], P [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G], Z [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.272
R-Value Work: 0.232
R-Value Observed: 0.232
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.773	α = 90
b = 140.78	β = 90
c = 268.419	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-06-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-06-17
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Refinement description