6MMO | pdb_00006mmo

Carbon regulatory PII-like protein SbtB from Cyanobium sp. 7001 bound to AMP

PDB DOI: https://doi.org/10.2210/pdb6MMO/pdb

Classification: SIGNALING PROTEIN
Organism(s): Cyanobium sp. PCC 7001
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-10-01 Released: 2019-09-18
Deposition Author(s): Kaczmarski, J.A., Jackson, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.252 (Depositor), 0.255 (DCC)
R-Value Work:
0.210 (Depositor), 0.212 (DCC)
R-Value Observed:
0.212 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Structure and function of SbtB from Cyanobium sp. 7001

Jackson, C., Kaczmarski, J.A., Price, D.

(2019) bioRxiv

Macromolecule Content

Total Structure Weight: 71.19 kDa
Atom Count: 4,337
Modeled Residue Count: 524
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon regulatory PII-like protein SbtB	A, B, C, D, E A, B, C, D, E, F	104	Cyanobium sp. PCC 7001	Mutation(s): 0 Gene Names: CPCC7001_1671

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F]	K [auth B] N [auth C] O [auth D] P [auth D] Q [auth E] K [auth B], N [auth C], O [auth D], P [auth D], Q [auth E], S [auth F]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain S [auth F] Interactions & Density Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain S [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain T [auth F] SDF format, chain R [auth E] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain T [auth F] MOL2 format, chain R [auth E] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain T [auth F] mmCIF format, chain R [auth E] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] L [auth B] M [auth B] H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], R [auth E], T [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth E] Focus chain T [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth E] Focus chain T [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.252 (Depositor), 0.255 (DCC)
R-Value Work: 0.210 (Depositor), 0.212 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.737	α = 97.91
b = 51.332	β = 102.55
c = 66.803	γ = 103.09

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-09-18

Deposition Author(s):

Kaczmarski, J.A.

Revision History (Full details and data files)

Version 1.0: 2019-09-18
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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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.