12NR | pdb_000012nr

Crystal structure of a GH26 enzyme (EiGH26a) in complex with mannose

• PDB DOI: https://doi.org/10.2210/pdb12NR/pdb

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


• Deposited: 2026-04-13 Released: 2026-09-09 
• Deposition Author(s): Miyamoto, R.Y., Oliveira, C.H.M., Morao, L.G., Martins, M.P., Murakami, M.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of a GH26 enzyme (EiGH26a) in complex with mannose

Persinoti, G.F., Martins, M.P., Silva, C.B.C., Streit, R.S.A., Paixao, D.A.A., Martins, G.H., Higasi, P.M.R., Braatz, G.M., Silva, M.K.P., Morao, L.G., Martins-Junior, J., Stoffel, F., Ciol, H., Noske, G.D., Miyamoto, R.Y., Oliveira, G.M., Martim, D.B., Oliveira, C.H.M., Almeida, O.A.C., Araujo, E.A., Andrade, M.O., Santos, C.A., Diogo, J.A., Wolf, L.D., Zanotto, J.V., Souza, A.R., Goncalves, F.A.C., Mello, D.M.D., Morais, M.A.B., Porto, J., Lombard, V., Giuseppe, P.O., Terrapon, N., Lemos, L.N., Henrissat, B., Carvalho, V.L., Silva, V.M.F., Murakami, M.T.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 39.92 kDa 
• Atom Count: 3,001 
• Modeled Residue Count: 323 
• Deposited Residue Count: 343 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 26	A	343	metagenome	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMA (Subject of Investigation/LOI)	B [auth A], C [auth A]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.895	α = 90
b = 65.31	β = 110.45
c = 83.667	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: 2026-09-09 
Deposition Author(s): Miyamoto, R.Y., Oliveira, C.H.M., Morao, L.G., Martins, M.P., 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	2022/03059-5
Sao Paulo Research Foundation (FAPESP)	Brazil	2021/09793-0
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	303898/2024-0
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	304440/2024-8

Revision History  

• Version 1.0: 2026-09-09
  Type: Initial release