8FJ8 | pdb_00008fj8

Crystal structure of Mn(2+),Ca(2+)-S100B

PDB DOI: https://doi.org/10.2210/pdb8FJ8/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Bos taurus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-19 Released: 2024-02-07
Deposition Author(s): Hunter, D.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.257 (Depositor), 0.258 (DCC)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Structural insights into ions binding to S100A1 versus S100B

Young, B., Sevdalis, S., Weber, D.J., Hunter, D., Zhuang, X., Varney, K., Melville, Z., Weber, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 10.55 kDa
Atom Count: 753
Modeled Residue Count: 90
Deposited Residue Count: 90
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-B	A	90	Bos taurus	Mutation(s): 0 Gene Names: S100B
UniProt
Find proteins for P02638 (Bos taurus) Explore P02638 Go to UniProtKB: P02638
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02638
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.257 (Depositor), 0.258 (DCC)
R-Value Work: 0.201 (Depositor), 0.201 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.598	α = 90
b = 90.602	β = 90
c = 58.087	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM129327

Revision History (Full details and data files)

Version 1.0: 2024-02-07
Type: Initial release

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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.