3F0N | pdb_00003f0n

Mus Musculus Mevalonate Pyrophosphate Decarboxylase

• PDB DOI: https://doi.org/10.2210/pdb3F0N/pdb

• Classification: LYASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-10-25 Released: 2008-11-25 
• Deposition Author(s): Walker, J.R., Davis, T., Vesterberg, A., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.221 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structure of Mus Musculus Mevalonate Pyrophosphate Decarboxylase

Walker, J.R., Davis, T., Vesterberg, A., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 91.81 kDa 
• Atom Count: 6,353 
• Modeled Residue Count: 760 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MEVALONATE PYROPHOSPHATE DECARBOXYLASE	A, B	414	Mus musculus	Mutation(s): 2  Gene Names: MVD EC: 4.1.1.33
UniProt & NIH Common Fund Data Resources
Find proteins for Q99JF5 (Mus musculus) Explore Q99JF5  Go to UniProtKB:  Q99JF5
IMPC:  MGI:2179327

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.221 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.619	α = 90
b = 139.619	β = 90
c = 88.719	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Walker, J.R., Davis, T., Vesterberg, A., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description