1ZT9 | pdb_00001zt9

E. coli trp repressor, tetragonal crystal form

PDB DOI: https://doi.org/10.2210/pdb1ZT9/pdb

Classification: TRANSCRIPTION
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-05-26 Released: 2006-05-09
Deposition Author(s): Lawson, C.L., Chin, A.S., Benoff, B., Yung, B.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.219 (Depositor), 0.230 (DCC)
R-Value Work:
0.164 (Depositor), 0.180 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Two association modes for E. coli trp repressor dimer-dimer interactions

Lawson, C.L., Chin, A.S., Benoff, B., Yung, B.H.

To be published.

Macromolecule Content

Total Structure Weight: 50.54 kDa
Atom Count: 3,906
Modeled Residue Count: 404
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trp operon repressor	A, B, C [auth D], D [auth E]	107	Escherichia coli	Mutation(s): 0 Gene Names: trpR, rtrY
UniProt
Find proteins for P0A881 (Escherichia coli (strain K12)) Explore P0A881 Go to UniProtKB: P0A881
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A881
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRP Query on TRP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth D] SDF format, chain P [auth E] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth D] MOL2 format, chain P [auth E] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth D] mmCIF format, chain P [auth E]	G [auth A], J [auth B], M [auth D], P [auth E]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth D] Focus chain P [auth E] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth D] Focus chain P [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain N [auth E] SDF format, chain O [auth E] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain N [auth E] mmCIF format, chain O [auth E]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth D] E [auth A], F [auth A], H [auth B], I [auth B], K [auth D], L [auth D], N [auth E], O [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth E] Focus chain O [auth E] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth E] Focus chain O [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.219 (Depositor), 0.230 (DCC)
R-Value Work: 0.164 (Depositor), 0.180 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.348	α = 90
b = 81.348	β = 90
c = 72.687	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-05-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-05-09
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

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E. coli trp repressor, tetragonal crystal form

Two association modes for E. coli trp repressor dimer-dimer interactions

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations