8BHU | pdb_00008bhu

Crystal Structure of SilF (Ag(I) form

PDB DOI: https://doi.org/10.2210/pdb8BHU/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-11-01 Released: 2023-11-15
Deposition Author(s): Lithgo, R.M., Carr, S.B., Quigley, A.M., Scott, D.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.230 (Depositor), 0.230 (DCC)
R-Value Work:
0.199 (Depositor), 0.199 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8BHU

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

Literature

Crystal Structure of SilF (apo form)

Lithgo, R.M., Carr, S.B., Quigley, A.M., Scott, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 78.87 kDa
Atom Count: 3,790
Modeled Residue Count: 469
Deposited Residue Count: 720
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SilF	A [auth AAA] B [auth BBB] C [auth CCC] D [auth DDD] E [auth EEE] A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE], F [auth FFF]	120	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A0A482M8M0 (Escherichia coli) Explore A0A482M8M0 Go to UniProtKB: A0A482M8M0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A482M8M0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain I [auth BBB] MOL2 format, chain I [auth BBB] mmCIF format, chain I [auth BBB]	I [auth BBB]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain I [auth BBB] Interactions & Density Focus chain I [auth BBB]
AG (Subject of Investigation/LOI) Query on AG Download:Ideal Coordinates CCD File SDF format, chain S [auth FFF] SDF format, chain Q [auth EEE] SDF format, chain N [auth DDD] SDF format, chain L [auth CCC] SDF format, chain J [auth BBB] SDF format, chain G [auth AAA] MOL2 format, chain S [auth FFF] MOL2 format, chain Q [auth EEE] MOL2 format, chain N [auth DDD] MOL2 format, chain L [auth CCC] MOL2 format, chain J [auth BBB] MOL2 format, chain G [auth AAA] mmCIF format, chain S [auth FFF] mmCIF format, chain Q [auth EEE] mmCIF format, chain N [auth DDD] mmCIF format, chain L [auth CCC] mmCIF format, chain J [auth BBB] mmCIF format, chain G [auth AAA]	G [auth AAA] J [auth BBB] L [auth CCC] N [auth DDD] Q [auth EEE] G [auth AAA], J [auth BBB], L [auth CCC], N [auth DDD], Q [auth EEE], S [auth FFF]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Focus chain J [auth BBB] Focus chain L [auth CCC] Focus chain N [auth DDD] Focus chain Q [auth EEE] Focus chain S [auth FFF] Interactions & Density Focus chain G [auth AAA] Focus chain J [auth BBB] Focus chain L [auth CCC] Focus chain N [auth DDD] Focus chain Q [auth EEE] Focus chain S [auth FFF]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain U [auth FFF] SDF format, chain T [auth FFF] SDF format, chain R [auth EEE] SDF format, chain P [auth DDD] SDF format, chain O [auth DDD] SDF format, chain M [auth CCC] SDF format, chain K [auth BBB] SDF format, chain H [auth AAA] MOL2 format, chain U [auth FFF] MOL2 format, chain T [auth FFF] MOL2 format, chain R [auth EEE] MOL2 format, chain P [auth DDD] MOL2 format, chain O [auth DDD] MOL2 format, chain M [auth CCC] MOL2 format, chain K [auth BBB] MOL2 format, chain H [auth AAA] mmCIF format, chain U [auth FFF] mmCIF format, chain T [auth FFF] mmCIF format, chain R [auth EEE] mmCIF format, chain P [auth DDD] mmCIF format, chain O [auth DDD] mmCIF format, chain M [auth CCC] mmCIF format, chain K [auth BBB] mmCIF format, chain H [auth AAA]	H [auth AAA] K [auth BBB] M [auth CCC] O [auth DDD] P [auth DDD] H [auth AAA], K [auth BBB], M [auth CCC], O [auth DDD], P [auth DDD], R [auth EEE], T [auth FFF], U [auth FFF]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth AAA] Focus chain K [auth BBB] Focus chain M [auth CCC] Focus chain O [auth DDD] Focus chain P [auth DDD] Focus chain R [auth EEE] Focus chain T [auth FFF] Focus chain U [auth FFF] Interactions & Density Focus chain H [auth AAA] Focus chain K [auth BBB] Focus chain M [auth CCC] Focus chain O [auth DDD] Focus chain P [auth DDD] Focus chain R [auth EEE] Focus chain T [auth FFF] Focus chain U [auth FFF]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.230 (Depositor), 0.230 (DCC)
R-Value Work: 0.199 (Depositor), 0.199 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.937	α = 90
b = 81.594	β = 90
c = 95.785	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M008770/1
Wellcome Trust	United Kingdom	202892/Z/16/Z

Revision History (Full details and data files)

Version 1.0: 2023-11-15
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, 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.