1Z5N
Crystal structure of MTA/AdoHcy nucleosidase Glu12Gln mutant complexed with 5-methylthioribose and adenine
- PDB DOI: https://doi.org/10.2210/pdb1Z5N/pdb
- Classification: HYDROLASE
- Organism(s): Escherichia coli
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes 
- Deposited: 2005-03-18 Released: 2005-10-04 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.252 
- R-Value Work: 0.205 
- R-Value Observed: 0.205 
This is version 2.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
MTA/SAH nucleosidase | 242 | Escherichia coli | Mutation(s): 1  Gene Names: mtnN, mtn, pfs EC: 3.2.2.9 | ||
UniProt | |||||
Find proteins for P0AF12 (Escherichia coli (strain K12)) Explore P0AF12  Go to UniProtKB:  P0AF12 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0AF12 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SR1 Query on SR1 | C [auth A], E [auth B] | 5-S-methyl-5-thio-alpha-D-ribofuranose C6 H12 O4 S OLVVOVIFTBSBBH-KAZBKCHUSA-N | |||
ADE Query on ADE | D [auth A], F [auth B] | ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.252 
- R-Value Work: 0.205 
- R-Value Observed: 0.205 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 51.68 | α = 90 |
b = 69.46 | β = 90 |
c = 128.36 | γ = 90 |
Software Name | Purpose |
---|---|
CrystalClear | data collection |
d*TREK | data reduction |
CNS | refinement |
CrystalClear | data reduction |
d*TREK | data scaling |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2005-10-04  Deposition Author(s): Lee, J.E., Smith, G.D., Horvatin, C., Huang, D.J.T., Cornell, K.A., Riscoe, M.K., Howell, P.L.
Revision History (Full details and data files)
- Version 1.0: 2005-10-04
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2021-10-20
Changes: Database references, Structure summary - Version 2.2: 2023-08-23
Changes: Data collection, Refinement description