3MEZ | pdb_00003mez

X-ray structural analysis of a mannose specific lectin from dutch crocus (crocus vernus)

• PDB DOI: https://doi.org/10.2210/pdb3MEZ/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Crocus vernus
• Mutation(s): No 


• Deposited: 2010-04-01 Released: 2011-06-22 
• Deposition Author(s): Akrem, A., Meyer, A., Perbandt, M., Voelter, W., Buck, F., Betzel, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

X-ray structural analysis of a mannose specific lectin from dutch crocus (crocus vernus)

Akrem, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 49.63 kDa 
• Atom Count: 3,765 
• Modeled Residue Count: 446 
• Deposited Residue Count: 448 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannose-specific lectin 3 chain 1	A, C	111	Crocus vernus	Mutation(s): 0
UniProt
Find proteins for P86626 (Crocus vernus) Explore P86626  Go to UniProtKB:  P86626

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannose-specific lectin 3 chain 2	B, D	113	Crocus vernus	Mutation(s): 0
UniProt
Find proteins for P86626 (Crocus vernus) Explore P86626  Go to UniProtKB:  P86626

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], L [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth D], O [auth D]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.422	α = 90
b = 98.154	β = 90
c = 105.827	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SOLVE	phasing
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-22 
Deposition Author(s): Akrem, A., Meyer, A., Perbandt, M., Voelter, W., Buck, F., Betzel, C.

Revision History  

• Version 1.0: 2011-06-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-12-25
  Changes: Data collection
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary