3G1U | pdb_00003g1u

Crystal structure of Leishmania major S-adenosylhomocysteine hydrolase

• PDB DOI: https://doi.org/10.2210/pdb3G1U/pdb

• Classification: HYDROLASE
• Organism(s): Leishmania major
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-30 Released: 2009-02-10 
• Deposition Author(s): Siponen, M.I., Welin, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Schutz, P., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Wisniewska, M., Schueler, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.232 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Leishmania major S-adenosylhomocysteine hydrolase

Siponen, M.I., Welin, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Schutz, P., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Wisniewska, M., Schueler, H.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 195.26 kDa 
• Atom Count: 13,715 
• Modeled Residue Count: 1,666 
• Deposited Residue Count: 1,748 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D	437	Leishmania major	Mutation(s): 0  Gene Names: LmjF36.3910, SAH EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt
Find proteins for Q4Q124 (Leishmania major) Explore Q4Q124  Go to UniProtKB:  Q4Q124

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	F [auth A], H [auth B], J [auth C], L [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ADN	E [auth A], G [auth B], I [auth C], K [auth D]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.232 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.38	α = 87.02
b = 82.47	β = 71.41
c = 83.88	γ = 74

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-10 
Deposition Author(s): Siponen, M.I., Welin, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Schutz, P., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Wisniewska, M., Schueler, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description