7CUD | pdb_00007cud

Crystal structure of HID in the unbound form

PDB DOI: https://doi.org/10.2210/pdb7CUD/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Streptococcus pyogenes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-08-22 Released: 2021-07-07
Deposition Author(s): Caaveiro, J.M.M., Hoshino, M., Tsumoto, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.206 (Depositor), 0.214 (DCC)
R-Value Work:
0.155 (Depositor), 0.169 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7CUD

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

Literature

Structural basis for the recognition of human hemoglobin by the Shr protein from Streptococcus pyogenes

Caaveiro, J.M.M., Hoshino, M., Senoo, A., Nakakido, M., Nagatoishi, S., Tame, J.R.H., Tsumoto, K.

To be published.

Macromolecule Content

Total Structure Weight: 13.78 kDa
Atom Count: 1,027
Modeled Residue Count: 116
Deposited Residue Count: 124
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid ABC transporter substrate-binding protein	A	124	Streptococcus pyogenes	Mutation(s): 0 Gene Names: shr, inlA_2, G3M98_06270, GTK50_07335, SAMEA3919037_01262
UniProt
Find proteins for Q99YA0 (Streptococcus pyogenes serotype M1) Explore Q99YA0 Go to UniProtKB: Q99YA0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99YA0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BR Query on BR 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]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.206 (Depositor), 0.214 (DCC)
R-Value Work: 0.155 (Depositor), 0.169 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.07	α = 90
b = 76.07	β = 90
c = 33.92	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-07

Deposition Author(s):

Caaveiro, J.M.M.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	15K06962

Revision History (Full details and data files)

Version 1.0: 2021-07-07
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-09-17
Changes: Advisory, Derived calculations, Structure summary

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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.