3D4R

CRYSTAL STRUCTURE OF a DUF2118 family protein (MMP0046) FROM METHANOCOCCUS MARIPALUDIS AT 2.20 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3D4R/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Methanococcus maripaludis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-14 Released: 2008-07-08 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Crystal structure of Domain of Unknown Function from the Pfam-B_34464 Family (NP_987166.1) from Methanococcus maripaludis JJ (DSM 2067) at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 119.61 kDa 
• Atom Count: 8,079 
• Modelled Residue Count: 940 
• Deposited Residue Count: 1,014 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Domain of Unknown Function from the Pfam-B_34464 Family	A, B, C, D, E, F	169	Methanococcus maripaludis	Mutation(s): 0  Gene Names: NP_987166.1, MMP0046
UniProt
Find proteins for Q6M171 (Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL)) Explore Q6M171  Go to UniProtKB:  Q6M171

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	L [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], I [auth C], J [auth C], K [auth D], M [auth E], N [auth E], O [auth F], P [auth F], Q [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M33D4R

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.877	α = 90
b = 109.858	β = 90
c = 135.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-08 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-07-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary