2XPV | pdb_00002xpv

TetR(D) in complex with minocycline and magnesium.

PDB DOI: https://doi.org/10.2210/pdb2XPV/pdb

Classification: TRANSCRIPTION
Organism(s): Escherichia coli
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2010-08-30 Released: 2011-09-07
Deposition Author(s): Dalm, D., Proft, J., Palm, G.J., Hinrichs, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.201 (Depositor), 0.212 (DCC)
R-Value Work:
0.185 (Depositor)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Tetr(D) in Complex with Minocycline.

Dalm, D., Palm, G.J., Proft, J., Hinrichs, W.

To be published.

Macromolecule Content

Total Structure Weight: 24.05 kDa
Atom Count: 1,987
Modeled Residue Count: 199
Deposited Residue Count: 207
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TETRACYCLINE REPRESSOR PROTEIN CLASS D	A	207	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ACT4 (Escherichia coli) Explore P0ACT4 Go to UniProtKB: P0ACT4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ACT4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MIY Query on MIY Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE C₂₃ H₂₇ N₃ O₇ DYKFCLLONBREIL-KVUCHLLUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.201 (Depositor), 0.212 (DCC)
R-Value Work: 0.185 (Depositor)
R-Value Observed: 0.186 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.686	α = 90
b = 68.686	β = 90
c = 178.673	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-09-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-07
Type: Initial release
Version 1.1: 2011-09-21
Changes: Atomic model
Version 1.2: 2019-07-24
Changes: Data collection, Derived calculations
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary

2XPV | pdb_00002xpv

TetR(D) in complex with minocycline and magnesium.

Literature

Tetr(D) in Complex with Minocycline.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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