3DP7 | pdb_00003dp7

CRYSTAL STRUCTURE OF SAM-dependent methyltransferase from Bacteroides vulgatus ATCC 8482

• PDB DOI: https://doi.org/10.2210/pdb3DP7/pdb

• Classification: TRANSFERASE
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-07 Released: 2008-07-29 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Ramagopal, U., Meyer, A.J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

CRYSTAL STRUCTURE OF SAM-dependent methyltransferase from Bacteroides vulgatus ATCC 8482

MALASHKEVICH, V.N., TORO, R., Ramagopal, U., MEYER, A.J., SAUDER, J.M., BURLEY, S.K., ALMO, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 82.87 kDa 
• Atom Count: 5,694 
• Modeled Residue Count: 701 
• Deposited Residue Count: 726 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM-dependent methyltransferase	A, B	363	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_1015
UniProt
Find proteins for A6KZ44 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6KZ44  Go to UniProtKB:  A6KZ44

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.804	α = 90
b = 130.804	β = 90
c = 122.747	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-29 
Deposition Author(s): Malashkevich, V.N., Toro, R., Ramagopal, U., Meyer, A.J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2012-04-11
  Changes: Data collection
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.6: 2024-02-21
  Changes: Data collection, Database references