8EBF | pdb_00008ebf

C-terminal (TPR) domain of LIC11990 from Leptospira interrogans

PDB DOI: https://doi.org/10.2210/pdb8EBF/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Leptospira interrogans serovar Copenhageni
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-08-31 Released: 2022-09-21
Deposition Author(s): Larrieux, N., Buschiazzo, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.278 (Depositor), 0.274 (DCC)
R-Value Work:
0.235 (Depositor), 0.231 (DCC)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Structure and function of a novel membrane-associated protein from Leptospira interrogans (gene LIC11990)

Wunder, E.A., Larrieux, N., Buschiazzo, A.

To be published.

Macromolecule Content

Total Structure Weight: 82.88 kDa
Atom Count: 5,377
Modeled Residue Count: 667
Deposited Residue Count: 718
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic membrane protein	A	718	Leptospira interrogans serovar Copenhageni	Mutation(s): 0 Gene Names: LIC_11990
UniProt
Find proteins for Q72QW8 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130)) Explore Q72QW8 Go to UniProtKB: Q72QW8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72QW8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain B [auth A]	B [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A], E [auth A], F [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.278 (Depositor), 0.274 (DCC)
R-Value Work: 0.235 (Depositor), 0.231 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.656	α = 90
b = 100.093	β = 90
c = 170.205	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-09-21
Type: Initial release
Version 1.1: 2024-05-22
Changes: Data collection

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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.