9P2D | pdb_00009p2d

Crystal structure of GH158(Pro) at 1.30 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb9P2D/pdb

• Classification: HYDROLASE
• Organism(s): metagenome
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-06-11 Released: 2026-03-11 
• Deposition Author(s): Spadeto, J.P.M., Martins, M.P., Araujo, E.A., Mandelli, F., Domingues, M.N., Santos, C.A., Santos, C.R., Morais, M.A.B., Murakami, M.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.194 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ProGH158 at 1.30 angstrom resolution

Spadeto, J.P.M., Martins, M.P., Araujo, E.A., Mandelli, F., Domingues, M.N., Santos, C.A., Santos, C.R., Morais, M.A.B., Murakami, M.T.

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

Macromolecule Content 

• Total Structure Weight: 46.78 kDa 
• Atom Count: 3,809 
• Modeled Residue Count: 406 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH158(Pro)	A	424	metagenome	Mutation(s): 0  EC: 3.2.1.39

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A], C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.194 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.108	α = 90
b = 70.557	β = 90
c = 115.538	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-03-11 
Deposition Author(s): Spadeto, J.P.M., Martins, M.P., Araujo, E.A., Mandelli, F., Domingues, M.N., Santos, C.A., Santos, C.R., Morais, M.A.B., Murakami, M.T.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2021/04891-3
Sao Paulo Research Foundation (FAPESP)	Brazil	2021/09793-0
Sao Paulo Research Foundation (FAPESP)	Brazil	2022/06298-0

Revision History  

• Version 1.0: 2026-03-11
  Type: Initial release