8IDV | pdb_00008idv

Crystal structure of Fic protein from Mycoplasma mycoides

• PDB DOI: https://doi.org/10.2210/pdb8IDV/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.297 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Fic protein from Mycoplasma mycoides

Zhang, H., Zhao, H.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 91.12 kDa 
• Atom Count: 6,057 
• Modeled Residue Count: 717 
• Deposited Residue Count: 760 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES (Subject of Investigation/LOI)	E [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG (Subject of Investigation/LOI)	F [auth B], G [auth C], H [auth C], I [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.297 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.6	α = 90
b = 120.6	β = 90
c = 165.4	γ = 120

Software Package:

Software Name	Purpose
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): Zhang, H., Zhao, H.F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31970152

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release