8SR2

particulate methane monooxygenase incubated with 4,4,4-trifluorobutanol

PDB DOI: https://doi.org/10.2210/pdb8SR2/pdb
EM Map EMD-40718: EMDB EMDataResource

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

Deposited: 2023-05-05 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: 2.36 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

Macromolecule Content

Total Structure Weight: 337.41 kDa
Atom Count: 22,885
Modelled Residue Count: 2,577
Deposited Residue Count: 2,763
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Particulate methane monooxygenase alpha subunit	A, D [auth E], E [auth I]	414	Methylococcus capsulatus str. Bath	Mutation(s): 0 Gene Names: pmoB1, pmoB, MCA1796, pmoB2, MCA2853 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G1UBD1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Particulate methane monooxygenase beta subunit	B, F [auth J], G [auth F]	247	Methylococcus capsulatus str. Bath	Mutation(s): 0 Gene Names: pmoA1, pmoA, MCA1797, pmoA2, MCA2854 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q607G3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ammonia monooxygenase/methane monooxygenase, subunit C family protein	C, H [auth G], I [auth K]	260	Methylococcus capsulatus str. Bath	Mutation(s): 0 Gene Names: pmoC1, MCA1798, MCA2855 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q603F1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLC Query on PLC Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BB [auth G] SDF format, chain CA [auth C] SDF format, chain FA [auth C] SDF format, chain FB [auth G] SDF format, chain IB [auth G] SDF format, chain JB [auth G] SDF format, chain LB [auth G] SDF format, chain M [auth B] SDF format, chain MA [auth J] SDF format, chain RB [auth K] SDF format, chain VA [auth F] SDF format, chain VB [auth K] SDF format, chain W [auth C] SDF format, chain XB [auth K] SDF format, chain SA [auth J] SDF format, chain UB [auth K] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BB [auth G] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain IB [auth G] MOL2 format, chain JB [auth G] MOL2 format, chain LB [auth G] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth J] MOL2 format, chain RB [auth K] MOL2 format, chain VA [auth F] MOL2 format, chain VB [auth K] MOL2 format, chain W [auth C] MOL2 format, chain XB [auth K] MOL2 format, chain SA [auth J] MOL2 format, chain UB [auth K] MOL2 format, chain Z [auth C]	AA [auth C] BB [auth G] CA [auth C] FA [auth C] FB [auth G] AA [auth C], BB [auth G], CA [auth C], FA [auth C], FB [auth G], IB [auth G], JB [auth G], LB [auth G], M [auth B], MA [auth J], RB [auth K], SA [auth J], UB [auth K], VA [auth F], VB [auth K], W [auth C], XB [auth K], Z [auth C]	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O		Interactions Focus chain AA [auth C] Focus chain BB [auth G] Focus chain CA [auth C] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain IB [auth G] Focus chain JB [auth G] Focus chain LB [auth G] Focus chain M [auth B] Focus chain MA [auth J] Focus chain RB [auth K] Focus chain SA [auth J] Focus chain UB [auth K] Focus chain VA [auth F] Focus chain VB [auth K] Focus chain W [auth C] Focus chain XB [auth K] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BB [auth G] Focus chain CA [auth C] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain IB [auth G] Focus chain JB [auth G] Focus chain LB [auth G] Focus chain M [auth B] Focus chain MA [auth J] Focus chain RB [auth K] Focus chain SA [auth J] Focus chain UB [auth K] Focus chain VA [auth F] Focus chain VB [auth K] Focus chain W [auth C] Focus chain XB [auth K] Focus chain Z [auth C]
P1O Query on P1O Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain MB [auth G] SDF format, chain N [auth B] SDF format, chain NA [auth J] SDF format, chain NB [auth G] SDF format, chain S [auth B] SDF format, chain TA [auth J] SDF format, chain UA [auth F] SDF format, chain WA [auth F] SDF format, chain YB [auth K] SDF format, chain ZB [auth K] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain MB [auth G] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth J] MOL2 format, chain NB [auth G] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth J] MOL2 format, chain UA [auth F] MOL2 format, chain WA [auth F] MOL2 format, chain YB [auth K] MOL2 format, chain ZB [auth K]	DA [auth C] EA [auth C] MB [auth G] N [auth B] NA [auth J] DA [auth C], EA [auth C], MB [auth G], N [auth B], NA [auth J], NB [auth G], S [auth B], TA [auth J], UA [auth F], WA [auth F], YB [auth K], ZB [auth K]	1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₂₈ H₅₇ N O₈ P MLKLDGSYMHFAOC-AREMUKBSSA-O		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain MB [auth G] Focus chain N [auth B] Focus chain NA [auth J] Focus chain NB [auth G] Focus chain S [auth B] Focus chain TA [auth J] Focus chain UA [auth F] Focus chain WA [auth F] Focus chain YB [auth K] Focus chain ZB [auth K] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain MB [auth G] Focus chain N [auth B] Focus chain NA [auth J] Focus chain NB [auth G] Focus chain S [auth B] Focus chain TA [auth J] Focus chain UA [auth F] Focus chain WA [auth F] Focus chain YB [auth K] Focus chain ZB [auth K]
HXG Query on HXG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain GB [auth G] SDF format, chain KB [auth G] SDF format, chain SB [auth K] SDF format, chain WB [auth K] SDF format, chain X [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain GB [auth G] MOL2 format, chain KB [auth G] MOL2 format, chain SB [auth K] MOL2 format, chain WB [auth K] MOL2 format, chain X [auth C]	BA [auth C] GB [auth G] KB [auth G] SB [auth K] WB [auth K] BA [auth C], GB [auth G], KB [auth G], SB [auth K], WB [auth K], X [auth C]	1,2-dihexanoyl-sn-glycero-3-phosphocholine C₂₀ H₄₁ N O₈ P DVZARZBAWHITHR-GOSISDBHSA-O		Interactions Focus chain BA [auth C] Focus chain GB [auth G] Focus chain KB [auth G] Focus chain SB [auth K] Focus chain WB [auth K] Focus chain X [auth C] Interactions & Density Focus chain BA [auth C] Focus chain GB [auth G] Focus chain KB [auth G] Focus chain SB [auth K] Focus chain WB [auth K] Focus chain X [auth C]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain HB [auth G] SDF format, chain IA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth I] SDF format, chain O [auth B] SDF format, chain OA [auth J] SDF format, chain P [auth B] SDF format, chain PA [auth J] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain TB [auth K] SDF format, chain XA [auth F] SDF format, chain Y [auth C] SDF format, chain YA [auth F] SDF format, chain ZA [auth F] SDF format, chain QA [auth J] SDF format, chain RA [auth J] MOL2 format, chain AB [auth F] MOL2 format, chain HB [auth G] MOL2 format, chain IA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth I] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth J] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain TB [auth K] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth F] MOL2 format, chain ZA [auth F] MOL2 format, chain QA [auth J] MOL2 format, chain RA [auth J]	AB [auth F] HB [auth G] IA [auth E] L [auth A] LA [auth I] AB [auth F], HB [auth G], IA [auth E], L [auth A], LA [auth I], O [auth B], OA [auth J], P [auth B], PA [auth J], Q [auth B], QA [auth J], R [auth B], RA [auth J], TB [auth K], XA [auth F], Y [auth C], YA [auth F], ZA [auth F]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain HB [auth G] Focus chain IA [auth E] Focus chain L [auth A] Focus chain LA [auth I] Focus chain O [auth B] Focus chain OA [auth J] Focus chain P [auth B] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain R [auth B] Focus chain RA [auth J] Focus chain TB [auth K] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain HB [auth G] Focus chain IA [auth E] Focus chain L [auth A] Focus chain LA [auth I] Focus chain O [auth B] Focus chain OA [auth J] Focus chain P [auth B] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain R [auth B] Focus chain RA [auth J] Focus chain TB [auth K] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain ZA [auth F]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain DB [auth G] SDF format, chain HA [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth I] SDF format, chain K [auth A] SDF format, chain KA [auth I] SDF format, chain PB [auth K] SDF format, chain QB [auth K] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain EB [auth G] SDF format, chain GA [auth E] MOL2 format, chain DB [auth G] MOL2 format, chain HA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth I] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth I] MOL2 format, chain PB [auth K] MOL2 format, chain QB [auth K] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain GA [auth E]	DB [auth G] EB [auth G] GA [auth E] HA [auth E] J [auth A] DB [auth G], EB [auth G], GA [auth E], HA [auth E], J [auth A], JA [auth I], K [auth A], KA [auth I], PB [auth K], QB [auth K], U [auth C], V [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain DB [auth G] Focus chain EB [auth G] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain J [auth A] Focus chain JA [auth I] Focus chain K [auth A] Focus chain KA [auth I] Focus chain PB [auth K] Focus chain QB [auth K] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain DB [auth G] Focus chain EB [auth G] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain J [auth A] Focus chain JA [auth I] Focus chain K [auth A] Focus chain KA [auth I] Focus chain PB [auth K] Focus chain QB [auth K] Focus chain U [auth C] Focus chain V [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CB [auth G] SDF format, chain OB [auth K] SDF format, chain T [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain OB [auth K] MOL2 format, chain T [auth C]	CB [auth G], OB [auth K], T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CB [auth G] Focus chain OB [auth K] Focus chain T [auth C] Interactions & Density Focus chain CB [auth G] Focus chain OB [auth K] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.36 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-15

Deposition Author(s):

Tucci, F.J.

Rosenzweig, A.C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118035
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM111097
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM105538
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	F31ES034283
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008382
National Science Foundation (NSF, United States)	United States	MCB-1908587