8SQW

particulate methane monooxygenase crosslinked with 2,2,2-trifluoroethanol bound

  • Classification: OXIDOREDUCTASE
  • Organism(s): Methylococcus capsulatus str. Bath
  • Mutation(s): No 
  • Membrane Protein: Yes  MemProtMD

  • Deposited: 2023-05-04 Released: 2023-11-15 
  • Deposition Author(s): Tucci, F.J., Rosenzweig, A.C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Product analogue binding identifies the copper active site of particulate methane monooyxgenase

Tucci, F.J.Jodts, R.J.Hoffman, B.M.Rosenzweig, A.C.

(2023) Nat Catal 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Particulate methane monooxygenase alpha subunitA,
D [auth E],
E [auth I]
382Methylococcus capsulatus str. BathMutation(s): 0 
Gene Names: pmoB1pmoBMCA1796pmoB2MCA2853
EC: 1.14.18.3
Membrane Entity: Yes 
UniProt
Find proteins for G1UBD1 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore G1UBD1 
Go to UniProtKB:  G1UBD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1UBD1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Particulate methane monooxygenase beta subunitB,
F,
G [auth J]
241Methylococcus capsulatus str. BathMutation(s): 0 
Gene Names: pmoA1pmoAMCA1797pmoA2MCA2854
EC: 1.14.18.3
Membrane Entity: Yes 
UniProt
Find proteins for Q607G3 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore Q607G3 
Go to UniProtKB:  Q607G3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ607G3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ammonia monooxygenase/methane monooxygenase, subunit C family proteinC,
H [auth G],
I [auth K]
236Methylococcus capsulatus str. BathMutation(s): 0 
Gene Names: pmoC1MCA1798MCA2855
EC: 1.14.13.25
Membrane Entity: Yes 
UniProt
Find proteins for Q603F1 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore Q603F1 
Go to UniProtKB:  Q603F1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ603F1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLC
Query on PLC

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth J]
BB [auth G]
DB [auth G]
EA [auth C]
AA [auth C],
AB [auth J],
BB [auth G],
DB [auth G],
EA [auth C],
GB [auth G],
IB [auth G],
LA [auth F],
M [auth B],
MA [auth F],
MB [auth K],
OB [auth K],
RB [auth K],
T [auth B],
TB [auth K],
UA [auth J],
V [auth C],
Y [auth C]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
P1O
Query on P1O

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
JB [auth G]
KB [auth G]
N [auth B]
BA [auth C],
CA [auth C],
JB [auth G],
KB [auth G],
N [auth B],
NA [auth F],
S [auth B],
SA [auth F],
TA [auth J],
UB [auth K],
VA [auth J],
VB [auth K]
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C28 H57 N O8 P
MLKLDGSYMHFAOC-AREMUKBSSA-O
HXG
Query on HXG

Download Ideal Coordinates CCD File 
EB [auth G]
HB [auth G]
PB [auth K]
SB [auth K]
W [auth C]
EB [auth G],
HB [auth G],
PB [auth K],
SB [auth K],
W [auth C],
Z [auth C]
1,2-dihexanoyl-sn-glycero-3-phosphocholine
C20 H41 N O8 P
DVZARZBAWHITHR-GOSISDBHSA-O
D10
Query on D10

Download Ideal Coordinates CCD File 
FA [auth E]
FB [auth G]
IA [auth I]
J [auth A]
O [auth B]
FA [auth E],
FB [auth G],
IA [auth I],
J [auth A],
O [auth B],
OA [auth F],
P [auth B],
PA [auth F],
Q [auth B],
QA [auth F],
QB [auth K],
R [auth B],
RA [auth F],
WA [auth J],
X [auth C],
XA [auth J],
YA [auth J],
ZA [auth J]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
ETF (Subject of Investigation/LOI)
Query on ETF

Download Ideal Coordinates CCD File 
DA [auth C],
LB [auth G],
WB [auth K]
TRIFLUOROETHANOL
C2 H3 F3 O
RHQDFWAXVIIEBN-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
CB [auth G]
GA [auth E]
HA [auth E]
JA [auth I]
K [auth A]
CB [auth G],
GA [auth E],
HA [auth E],
JA [auth I],
K [auth A],
KA [auth I],
L [auth A],
NB [auth K],
U [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118035
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM111097
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM105538
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008382
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesT32GM008382
National Science Foundation (NSF, United States)United StatesMCB-1908587

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release