2NR4 | pdb_00002nr4

Crystal structure of FMN-bound protein MM1853 from Methanosarcina mazei, Pfam DUF447

• PDB DOI: https://doi.org/10.2210/pdb2NR4/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Methanosarcina mazei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-11-01 Released: 2006-11-07 
• Deposition Author(s): Bonanno, J.B., Gilmore, J., Bain, K.T., Lau, C., Wasserman, S., Smith, D., 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: 1.85 Å
• R-Value Free: 
  0.256 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Crystal structure of conserved FMN bound hypothetical protein from Methanosarcina mazei

Bonanno, J.B., Gilmore, J., Bain, K.T., Lau, C., Wasserman, S., Smith, D., 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: 48.84 kDa 
• Atom Count: 3,245 
• Modeled Residue Count: 373 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved hypothetical protein	A, B	213	Methanosarcina mazei	Mutation(s): 0  Gene Names: MM_1853
UniProt
Find proteins for Q8PVV4 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PVV4  Go to UniProtKB:  Q8PVV4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], D [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.256 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.334	α = 90
b = 139.334	β = 90
c = 55.391	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-07 
Deposition Author(s): Bonanno, J.B., Gilmore, J., Bain, K.T., Lau, C., Wasserman, S., Smith, D., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-11-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-10-24
  Changes: Structure summary
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.6: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.7: 2023-12-27
  Changes: Data collection, Database references