3DH0 | pdb_00003dh0

Crystal structure of a SAM dependent methyltransferase from Aquifex aeolicus

PDB DOI: https://doi.org/10.2210/pdb3DH0/pdb

Classification: TRANSFERASE
Organism(s): Aquifex aeolicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-16 Released: 2008-07-15
Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.296 (Depositor), 0.294 (DCC)
R-Value Work:
0.231 (Depositor), 0.230 (DCC)
R-Value Observed:
0.231 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a SAM dependent methyltransferase from Aquifex aeolicus

Agarwal, R., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 51.1 kDa
Atom Count: 3,152
Modeled Residue Count: 378
Deposited Residue Count: 438
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM dependent methyltransferase	A, B	219	Aquifex aeolicus	Mutation(s): 0 Gene Names: aq_1457
UniProt
Find proteins for O67440 (Aquifex aeolicus (strain VF5)) Explore O67440 Go to UniProtKB: O67440
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O67440
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.296 (Depositor), 0.294 (DCC)
R-Value Work: 0.231 (Depositor), 0.230 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.436	α = 90
b = 42.902	β = 106.74
c = 84.253	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-07-15

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-07-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-02-21
Changes: Data collection, Database references

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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.