1RLI | pdb_00001rli

The Structure of Trp Repressor Binding Protein from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb1RLI/pdb

Classification: Structural Genomics, protein binding
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-11-25 Released: 2004-04-13
Deposition Author(s): Kim, Y., Quartey, P., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.230 (Depositor), 0.232 (DCC)
R-Value Work:
0.196 (Depositor), 0.197 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure analysis of trp repressor binding protein from Bacillus subtilis

Kim, Y., Quartey, P., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 85.53 kDa
Atom Count: 5,714
Modeled Residue Count: 645
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trp Repressor Binding Protein	A, B, C, D	184	Bacillus subtilis	Mutation(s): 0 EC: 1
UniProt
Find proteins for P96726 (Bacillus subtilis (strain 168)) Explore P96726 Go to UniProtKB: P96726
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P96726
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT Query on PT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], M [auth C], N [auth C], O [auth C], P [auth D], Q [auth D], R [auth D]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	J [auth B], K [auth B], L [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.230 (Depositor), 0.232 (DCC)
R-Value Work: 0.196 (Depositor), 0.197 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.993	α = 90
b = 90.666	β = 97.02
c = 63.446	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
d*TREK	data reduction
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-04-13

Deposition Author(s):

Kim, Y.

Quartey, P.

Joachimiak, A.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2004-04-13
Type: Initial release
Version 1.1: 2008-04-29
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