1WTA | pdb_00001wta

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine from Aeropyrum pernix (R32 form)

PDB DOI: https://doi.org/10.2210/pdb1WTA/pdb

Classification: TRANSFERASE
Organism(s): Aeropyrum pernix K1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-11-18 Released: 2006-02-07
Deposition Author(s): Tsunoda, M., Murakami, Y., Nakamura, K.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.196 (Depositor)
R-Value Work:
0.164 (Depositor)
R-Value Observed:
0.166 (Depositor)

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This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine from Aeropyrum pernix (R32 form)

Tsunoda, M., Murakami, Y., Nakamura, K.T.

To be published.

Macromolecule Content

Total Structure Weight: 31.01 kDa
Atom Count: 2,507
Modeled Residue Count: 273
Deposited Residue Count: 275
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-methylthioadenosine phosphorylase	A	275	Aeropyrum pernix K1	Mutation(s): 0 EC: 2.4.2.28
UniProt
Find proteins for Q9YAQ8 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YAQ8 Go to UniProtKB: Q9YAQ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9YAQ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADE Query on ADE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain C [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.196 (Depositor)
R-Value Work: 0.164 (Depositor)
R-Value Observed: 0.166 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.15	α = 90
b = 78.15	β = 90
c = 230.43	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-02-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-02-07
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-11
Changes: Advisory, Refinement description
Version 1.4: 2017-11-01
Changes: Derived calculations
Version 1.5: 2024-11-20
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.