1QNP | pdb_00001qnp

The 3-D structure of a Trichoderma reesei b-mannanase from glycoside hydrolase family 5

• PDB DOI: https://doi.org/10.2210/pdb1QNP/pdb

• Classification: HYDROLASE
• Organism(s): Trichoderma reesei
• Expression System: Trichoderma reesei
• Mutation(s): No 


• Deposited: 1999-10-20 Released: 2000-10-19 
• Deposition Author(s): Sabini, E., Schubert, H., Murshudov, G., Wilson, K.S., Siika-Aho, M., Penttila, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.174 (Depositor) 
• R-Value Work: 
  0.127 (Depositor) 

Literature

The Three-Dimensional Structure of a Trichoderma Reesei Beta-Mannanase from Glycoside Hydrolase Family 5.

Sabini, E., Schubert, H., Murshudov, G., Wilson, K.S., Siika-Aho, M., Penttila, M.

(2000) Acta Crystallogr D Biol Crystallogr 56: 3

• PubMed: 10666621 
• DOI: https://doi.org/10.1107/s0907444999013943
• Primary Citation Related Structures: 
  1QNO, 1QNP, 1QNQ, 1QNR, 1QNS


• PubMed Abstract: 
  

  The crystal structure of the catalytic core domain of beta-mannanase from the fungus Trichoderma reesei has been determined at a resolution of 1.5 A. The structure was solved using the anomalous scattering from a single non-isomorphous platinum complex with two heavy-metal sites in space group P2(1). The map computed with the experimental phases was enhanced by the application of an automated model building and refinement procedure using the amplitudes and experimental phases as observations. This approach is expected to be of more general application. The structure of the native enzyme and complexes with Tris-HCl and mannobiose are also reported: the mannobiose binds in subsites +1 and +2. The structure is briefly compared with that of the homologous beta-mannanase from the bacterium Thermomonospora fusca.

---

Organizational Affiliation: 
• Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England.

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 38.82 kDa 
• Atom Count: 3,240 
• Modeled Residue Count: 344 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-1,4-B-D-MANNANASE	A	344	Trichoderma reesei	Mutation(s): 0  EC: 3.2.1.78
UniProt
Find proteins for Q99036 (Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30)) Explore Q99036  Go to UniProtKB:  Q99036
Glycosylation
Glycosylation Sites: 4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.174 (Depositor) 
• R-Value Work:  0.127 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.18	α = 90
b = 54.6	β = 111.23
c = 60.76	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-10-19 
Deposition Author(s): Sabini, E., Schubert, H., Murshudov, G., Wilson, K.S., Siika-Aho, M., Penttila, M.

Revision History  

• Version 1.0: 2000-10-19
  Type: Initial release
  
• Version 1.1: 2013-01-30
  Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Structure summary