1JRE | pdb_00001jre

DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN

PDB DOI: https://doi.org/10.2210/pdb1JRE/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2001-08-13 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: 2.65 Å
R-Value Free:
0.264 (Depositor), 0.258 (DCC)
R-Value Work:
0.229 (Depositor), 0.225 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

DNA Protection and Binding by E. Coli Dps Protein

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

To be published.

Macromolecule Content

Total Structure Weight: 226.9 kDa
Atom Count: 15,083
Modeled Residue Count: 1,871
Deposited Residue Count: 2,004
Unique protein chains: 1

Macromolecules

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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): 2 EC: 1.16
UniProt
Find proteins for P0ABT2 (Escherichia coli (strain K12)) Explore P0ABT2 Go to UniProtKB: P0ABT2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] 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 FA [auth H] SDF format, chain AA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] 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 FA [auth H] MOL2 format, chain AA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] 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 FA [auth H] mmCIF format, chain AA [auth E]	AA [auth E] FA [auth H] JA [auth K] N [auth A] O [auth A] AA [auth E], FA [auth H], JA [auth K], N [auth A], O [auth A], Q [auth B], R [auth B], T [auth C], U [auth C], W [auth D], X [auth D], Y [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain AA [auth E] Focus chain FA [auth H] 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 T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth H] 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 T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain V [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 HA [auth J] SDF format, chain GA [auth I] SDF format, chain EA [auth H] SDF format, chain DA [auth G] SDF format, chain CA [auth G] SDF format, chain BA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain V [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 HA [auth J] MOL2 format, chain GA [auth I] MOL2 format, chain EA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain V [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 HA [auth J] mmCIF format, chain GA [auth I] mmCIF format, chain EA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth F]	BA [auth F] CA [auth G] DA [auth G] EA [auth H] GA [auth I] BA [auth F], CA [auth G], DA [auth G], EA [auth H], GA [auth I], HA [auth J], IA [auth K], KA [auth L], M [auth A], P [auth B], S [auth C], V [auth D], Z [auth E]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain HA [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 V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain HA [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 V [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.264 (Depositor), 0.258 (DCC)
R-Value Work: 0.229 (Depositor), 0.225 (DCC)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.585	α = 90
b = 90.585	β = 90
c = 226.507	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

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: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-10-27
Changes: Database references, Derived calculations
Version 1.4: 2023-08-16
Changes: Data collection, Refinement description

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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.