1RUN | pdb_00001run

CATABOLITE GENE ACTIVATOR PROTEIN (CAP)/DNA COMPLEX + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

PDB DOI: https://doi.org/10.2210/pdb1RUN/pdb
NAKB: 1RUN

Classification: TRANSCRIPTION/DNA
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1996-05-26 Released: 1997-01-10
Deposition Author(s): Parkinson, G.N., Gunasekera, A., Vojtechovsky, J., Zhang, X., Kunkel, T.A., Berman, H.M., Ebright, R.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Work:
0.207 (Depositor), 0.214 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Aromatic hydrogen bond in sequence-specific protein DNA recognition.

Parkinson, G., Gunasekera, A., Vojtechovsky, J., Zhang, X., Kunkel, T.A., Berman, H., Ebright, R.H.

(1996) Nat Struct Biol 3: 837-841

PubMed: 8836098 Search on PubMed
DOI: https://doi.org/10.1038/nsb1096-837
Primary Citation Related Structures:
1RUN, 1RUO

Macromolecule Content

Total Structure Weight: 66.75 kDa
Atom Count: 4,654
Modeled Residue Count: 460
Deposited Residue Count: 480
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CATABOLITE GENE ACTIVATOR PROTEIN (CAP))	E [auth A], F [auth B]	209	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ACJ8 (Escherichia coli (strain K12)) Explore P0ACJ8 Go to UniProtKB: P0ACJ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ACJ8
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
DNA (5'-D(GPCPGPAPAPAPAPAPTPGPTPGPAPT)-3')	A [auth C], C [auth E]	14	N/A
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(CPTPAPGPAPTPCPAPCPAPTPTPTPTPTPCP*G )-3')	B [auth D], D [auth F]	17	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CMP Query on CMP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C₁₀ H₁₂ N₅ O₆ P IVOMOUWHDPKRLL-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Work: 0.207 (Depositor), 0.214 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.93	α = 90
b = 152.8	β = 90
c = 76	γ = 90

Software Package:

Software Name	Purpose
PURDUE	data collection
X-PLOR	refinement
PURDUE	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 1997-01-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1997-01-10
Type: Initial release
Version 1.1: 2008-05-22
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations