1FZ9

Methane monooxygenase hydroxylase, form II cocrystallized with iodoethane


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Xenon and halogenated alkanes track putative substrate binding cavities in the soluble methane monooxygenase hydroxylase.

Whittington, D.A.Rosenzweig, A.C.Frederick, C.A.Lippard, S.J.

(2001) Biochemistry 40: 3476-3482

  • Primary Citation of Related Structures:  1FZ8, 1FZH, 1FZI

  • PubMed Abstract: 
  • To investigate the role of protein cavities in facilitating movement of the substrates, methane and dioxygen, in the soluble methane monooxygenase hydroxylase (MMOH), we determined the X-ray structures of MMOH from Methylococcus capsulatus (Bath) coc ...

    To investigate the role of protein cavities in facilitating movement of the substrates, methane and dioxygen, in the soluble methane monooxygenase hydroxylase (MMOH), we determined the X-ray structures of MMOH from Methylococcus capsulatus (Bath) cocrystallized with dibromomethane or iodoethane, or by using crystals pressurized with xenon gas. The halogenated alkanes bind in two cavities within the alpha-subunit that extend from one surface of the protein to the buried dinuclear iron active site. Two additional binding sites were located in the beta-subunit. Pressurization of two crystal forms of MMOH with xenon resulted in the identification of six binding sites located exclusively in the alpha-subunit. These results indicate that hydrophobic species bind preferentially in preexisting cavities in MMOH and support the hypothesis that such cavities may play a functional role in sequestering and enhancing the availability of the physiological substrates for reaction at the active site.


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHANE MONOOXYGENASE COMPONENT A, ALPHA CHAIN
A, B
527Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)Gene Names: mmoX
EC: 1.14.13.25
Find proteins for P22869 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Go to UniProtKB:  P22869
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
METHANE MONOOXYGENASE COMPONENT A, BETA CHAIN
C, D
389Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)Gene Names: mmoY
EC: 1.14.13.25
Find proteins for P18798 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Go to UniProtKB:  P18798
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
METHANE MONOOXYGENASE COMPONENT A, GAMMA CHAIN
E, F
170Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)Gene Names: mmoZ
EC: 1.14.13.25
Find proteins for P11987 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Go to UniProtKB:  P11987
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
ETI
Query on ETI

Download SDF File 
Download CCD File 
A, B, C, D
IODOETHANE
C2 H5 I
HVTICUPFWKNHNG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.220α = 90.00
b = 172.220β = 90.00
c = 221.190γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance