5ZXA

Crystal structure of fibronectin-binding protein Apa mutant from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb5ZXA/pdb

Classification: PROTEIN BINDING
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-05-18 Released: 2019-05-29
Deposition Author(s): Gao, J., Liu, W.D., Chen, C.C., Guo, R.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.181
R-Value Work: 0.163
R-Value Observed: 0.164

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Functional and structural investigations of fibronectin-binding protein Apa from Mycobacterium tuberculosis.

Kuo, C.J., Gao, J., Huang, J.W., Ko, T.P., Zhai, C., Ma, L., Liu, W., Dai, L., Chang, Y.F., Chen, T.H., Hu, Y., Yu, X., Guo, R.T., Chen, C.C.

(2019) Biochim Biophys Acta Gen Subj 1863: 1351-1359

PubMed: 31175911 Search on PubMed
DOI: https://doi.org/10.1016/j.bbagen.2019.06.003
Primary Citation of Related Structures:
5ZX9, 5ZXA

PubMed Abstract:
Alanine and proline-rich protein (Apa) is a secreted antigen of Mycobacterium spp. which involves in stimulating immune responses and adhering to host cells by binding to fibronectin (Fn). Here, we report the crystal structure of Apa from Mycobacterium tuberculosis (Mtb) and its Fn-binding characteristics.

Organizational Affiliation

Department of Veterinary Medicine, National Chung Hsing University, Taichung 402, Taiwan.

Macromolecule Content

Total Structure Weight: 33.07 kDa
Atom Count: 1,400
Modelled Residue Count: 161
Deposited Residue Count: 325
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine and proline-rich secreted protein Apa	A	325	Mycobacterium tuberculosis H37Rv	Mutation(s): 1 Gene Names: 1860c
UniProt
Find proteins for P9WIR7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIR7 Go to UniProtKB: P9WIR7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WIR7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HG Query on HG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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: 1.77 Å
R-Value Free: 0.181
R-Value Work: 0.163
R-Value Observed: 0.164
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.028	α = 90
b = 118.028	β = 90
c = 118.852	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
CNS	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-05-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-05-29
Type: Initial release
Version 1.1: 2019-12-11
Changes: Database references, Structure summary
Version 1.2: 2024-03-27
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.