8IK1 | pdb_00008ik1

EstL5 in complex of PMSF

• PDB DOI: https://doi.org/10.2210/pdb8IK1/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus sp. PA-3
• Expression System: Escherichia
• Mutation(s): No 


• Deposited: 2023-02-28 Released: 2023-03-29 
• Deposition Author(s): Chen, R., Zhang, Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.250 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

EstL5 in complex of PMSF

Chen, R., Zhang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 52.02 kDa 
• Atom Count: 3,287 
• Modeled Residue Count: 412 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDSL family lipase	A, B	230	Geobacillus sp. PA-3	Mutation(s): 0  Gene Names: GEPA3_1571

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEZ (Subject of Investigation/LOI)	C [auth A], D [auth B]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEB	A, B	L-PEPTIDE LINKING	C10 H13 N O5 S		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.250 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.153	α = 90
b = 105.153	β = 90
c = 128.001	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-29 
Deposition Author(s): Chen, R., Zhang, Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2020YFA0907702

Revision History  

• Version 1.0: 2023-03-29
  Type: Initial release
  
• Version 2.0: 2023-06-21
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary