6IXX | pdb_00006ixx

Crystal structure of a complex between psychrophilic marine protease MP and its inhibitor LupI

• PDB DOI: https://doi.org/10.2210/pdb6IXX/pdb

• Classification: HYDROLASE/INIHBITOR
• Organism(s): Flavobacterium sp. YS-80-122
• Mutation(s): No 


• Deposited: 2018-12-12 Released: 2019-12-18 
• Deposition Author(s): Hao, J.H., Zhang, L.H.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a complex between psychrophilic marine protease MP and its inhibitor LupI

Hao, J.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 59.57 kDa 
• Atom Count: 4,428 
• Modeled Residue Count: 560 
• Deposited Residue Count: 560 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkaline metalloprotease	A	463	Flavobacterium sp. YS-80-122	Mutation(s): 0
UniProt
Find proteins for D0VMS8 (Flavobacterium sp. YS-80-122) Explore D0VMS8  Go to UniProtKB:  D0VMS8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LupI	B [auth I]	97	Flavobacterium sp. YS-80-122	Mutation(s): 0
UniProt
Find proteins for G3MEU6 (Flavobacterium sp. YS-80-122) Explore G3MEU6  Go to UniProtKB:  G3MEU6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	K [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.664	α = 90
b = 51.852	β = 97.68
c = 102.142	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-18 
Deposition Author(s): Hao, J.H., Zhang, L.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	41376175

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary