7L71 | pdb_00007l71

Crystal Structure of the PDZ Domain of the Serine Peptidase HtrA from Streptococcus agalactiae.

PDB DOI: https://doi.org/10.2210/pdb7L71/pdb

Classification: PROTEIN BINDING
Organism(s): Streptococcus agalactiae A909
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-12-24 Released: 2021-12-01
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.97 Å
R-Value Free:
0.150 (Depositor), 0.150 (DCC)
R-Value Work:
0.139 (Depositor), 0.140 (DCC)
R-Value Observed:
0.140 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the PDZ Domain of the Serine Peptidase HtrA from Streptococcus agalactiae.

Minasov, G., Shuvalova, L., Kiryukhina, O., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 12.5 kDa
Atom Count: 1,057
Modelled Residue Count: 108
Deposited Residue Count: 114
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease	A	114	Streptococcus agalactiae A909	Mutation(s): 0 Gene Names: HtrA
UniProt
Find proteins for Q8DWP1 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)) Explore Q8DWP1 Go to UniProtKB: Q8DWP1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DWP1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.97 Å
R-Value Free: 0.150 (Depositor), 0.150 (DCC)
R-Value Work: 0.139 (Depositor), 0.140 (DCC)
R-Value Observed: 0.140 (Depositor)

Diffraction Data: https://doi.org/10.18430/m37l71

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.878	α = 90
b = 29.33	β = 101.45
c = 35.827	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2021-12-01

Deposition Author(s):

Satchell, K.J.F.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2021-12-01
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary

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.