3GPI | pdb_00003gpi

Structure of putative NAD-dependent epimerase/dehydratase from methylobacillus flagellatus

• PDB DOI: https://doi.org/10.2210/pdb3GPI/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Methylobacillus flagellatus KT
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-23 Released: 2009-04-21 
• Deposition Author(s): Ramagopal, U.A., Morano, C., 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: 1.44 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Structure of putative NAD-dependent epimerase/dehydratase from methylobacillus flagellatus

Ramagopal, U.A., Morano, C., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.97 kDa 
• Atom Count: 2,391 
• Modeled Residue Count: 273 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent epimerase/dehydratase	A	286	Methylobacillus flagellatus KT	Mutation(s): 0  Gene Names: Mfla_2045
UniProt
Find proteins for Q1GZM5 (Methylobacillus flagellatus (strain ATCC 51484 / DSM 6875 / VKM B-1610 / KT)) Explore Q1GZM5  Go to UniProtKB:  Q1GZM5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.574	α = 90
b = 68.892	β = 90
c = 96.141	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXE	model building
SHELXD	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Ramagopal, U.A., Morano, C., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-04-21
  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: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references