7YLQ | pdb_00007ylq

Crystal structure of Microcystinase C from Sphingomonas sp. ACM-3962 at 2.6 A resolution

• PDB DOI: https://doi.org/10.2210/pdb7YLQ/pdb

• Classification: HYDROLASE
• Organism(s): Sphingomonas sp. ACM-3962
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-26 Released: 2023-08-09 
• Deposition Author(s): Guo, X., Li, Z., Ding, W., Yin, P., Feng, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Crystal structure of Microcystin C from Sphingomonas sp. ACM-3962 at 2.6 A resolution

Guo, X., Li, Z., Ding, W., Yin, P., Feng, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 111.24 kDa 
• Atom Count: 7,379 
• Modeled Residue Count: 951 
• Deposited Residue Count: 1,024 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microcystinase C	A, B	512	Sphingomonas sp. ACM-3962	Mutation(s): 0  Gene Names: mlrC
UniProt
Find proteins for Q93CA6 (Sphingomonas sp) Explore Q93CA6  Go to UniProtKB:  Q93CA6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.43	α = 90
b = 138.43	β = 90
c = 275.572	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Guo, X., Li, Z., Ding, W., Yin, P., Feng, L.

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

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection