8IDW | pdb_00008idw

Crystal structure of Fic protein from Mycoplasma mycoides in complex with AMPPNP

PDB DOI: https://doi.org/10.2210/pdb8IDW/pdb

Classification: TRANSFERASE
Organism(s): Mycoplasma mycoides subsp. capri
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-14 Released: 2024-08-14
Deposition Author(s): Zhang, H., Zhao, H.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.251 (Depositor), 0.263 (DCC)
R-Value Work:
0.203 (Depositor)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Fic protein from Mycoplasma mycoides in complex with AMPPNP

Zhang, H., Zhao, H.F.

To be published.

Macromolecule Content

Total Structure Weight: 92.58 kDa
Atom Count: 6,543
Modeled Residue Count: 733
Deposited Residue Count: 760
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell filamentation protein Fic	A, B, C, D	190	Mycoplasma mycoides subsp. capri	Mutation(s): 0 Gene Names: MMC68J_00751

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AN2 (Subject of Investigation/LOI) Query on AN2 Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], J [auth C], N [auth D]	AMP PHOSPHORAMIDATE C₁₀ H₁₆ N₆ O₉ P₂ FQMDCEJHLOLKLI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain N [auth D]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B]	I [auth B], L [auth C], M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], K [auth C], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D]