3OAA

Structure of the E.coli F1-ATP synthase inhibited by subunit Epsilon

PDB DOI: https://doi.org/10.2210/pdb3OAA/pdb

Classification: Hydrolase/Transport protein
Organism(s): Escherichia coli DH1
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes mpstruc

Deposited: 2010-08-05 Released: 2011-05-25
Deposition Author(s): Cingolani, G., Duncan, T.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.26 Å
R-Value Free: 0.265
R-Value Work: 0.243
R-Value Observed: 0.243

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for inhibition of bacterial ATP synthase by subunit epsilon of the rotor stalk

Cingolani, G., Duncan, T.M.

To be published.

Macromolecule Content

Total Structure Weight: 1,461.92 kDa
Atom Count: 99,573
Modelled Residue Count: 13,028
Deposited Residue Count: 13,360
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	A AA [auth a] B C I A, AA [auth a], B, C, I, J, K, Q, R, S, Y, Z	513	Escherichia coli DH1	Mutation(s): 0 Gene Names: atpA, EcDH1_4233 EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P0ABB0 (Escherichia coli (strain K12)) Explore P0ABB0 Go to UniProtKB: P0ABB0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABB0
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	BA [auth b] CA [auth c] D DA [auth d] E BA [auth b], CA [auth c], D, DA [auth d], E, F, L, M, N, T, U, V	459	Escherichia coli DH1	Mutation(s): 1 Gene Names: atpD, EcDH1_4235 EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P0ABB4 (Escherichia coli (strain K12)) Explore P0ABB4 Go to UniProtKB: P0ABB4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABB4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase gamma chain	EA [auth e], G, O, W	286	Escherichia coli DH1	Mutation(s): 0 Gene Names: EcDH1_4234 Membrane Entity: Yes
UniProt
Find proteins for P0ABA6 (Escherichia coli (strain K12)) Explore P0ABA6 Go to UniProtKB: P0ABA6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABA6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase epsilon chain	FA [auth f], H, P, X	138	Escherichia coli DH1	Mutation(s): 0 Gene Names: atpC, EcDH1_4236 Membrane Entity: Yes
UniProt
Find proteins for P0A6E6 (Escherichia coli (strain K12)) Explore P0A6E6 Go to UniProtKB: P0A6E6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6E6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain GB [auth Q] SDF format, chain IA [auth B] SDF format, chain IB [auth R] SDF format, chain KA [auth C] SDF format, chain KB [auth S] SDF format, chain SB [auth Y] SDF format, chain TA [auth I] SDF format, chain UB [auth Z] SDF format, chain VA [auth J] SDF format, chain WB [auth a] SDF format, chain XA [auth K] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth Q] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth R] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth S] MOL2 format, chain SB [auth Y] MOL2 format, chain TA [auth I] MOL2 format, chain UB [auth Z] MOL2 format, chain VA [auth J] MOL2 format, chain WB [auth a] MOL2 format, chain XA [auth K] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth Q] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth R] mmCIF format, chain KA [auth C] mmCIF format, chain KB [auth S] mmCIF format, chain SB [auth Y] mmCIF format, chain TA [auth I] mmCIF format, chain UB [auth Z] mmCIF format, chain VA [auth J] mmCIF format, chain WB [auth a] mmCIF format, chain XA [auth K]	GA [auth A] GB [auth Q] IA [auth B] IB [auth R] KA [auth C] GA [auth A], GB [auth Q], IA [auth B], IB [auth R], KA [auth C], KB [auth S], SB [auth Y], TA [auth I], UB [auth Z], VA [auth J], WB [auth a], XA [auth K]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain GA [auth A] Focus chain GB [auth Q] Focus chain IA [auth B] Focus chain IB [auth R] Focus chain KA [auth C] Focus chain KB [auth S] Focus chain SB [auth Y] Focus chain TA [auth I] Focus chain UB [auth Z] Focus chain VA [auth J] Focus chain WB [auth a] Focus chain XA [auth K] Interactions & Density Focus chain GA [auth A] Focus chain GB [auth Q] Focus chain IA [auth B] Focus chain IB [auth R] Focus chain KA [auth C] Focus chain KB [auth S] Focus chain SB [auth Y] Focus chain TA [auth I] Focus chain UB [auth Z] Focus chain VA [auth J] Focus chain WB [auth a] Focus chain XA [auth K]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain MA [auth D] SDF format, chain MB [auth T] SDF format, chain YB [auth b] SDF format, chain ZA [auth L] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth T] MOL2 format, chain YB [auth b] MOL2 format, chain ZA [auth L] mmCIF format, chain MA [auth D] mmCIF format, chain MB [auth T] mmCIF format, chain YB [auth b] mmCIF format, chain ZA [auth L]	MA [auth D], MB [auth T], YB [auth b], ZA [auth L]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain MA [auth D] Focus chain MB [auth T] Focus chain YB [auth b] Focus chain ZA [auth L] Interactions & Density Focus chain MA [auth D] Focus chain MB [auth T] Focus chain YB [auth b] Focus chain ZA [auth L]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AC [auth b] SDF format, chain BB [auth L] SDF format, chain BC [auth c] SDF format, chain CB [auth M] SDF format, chain CC [auth d] SDF format, chain DB [auth N] SDF format, chain EB [auth O] SDF format, chain FB [auth P] SDF format, chain OA [auth D] SDF format, chain OB [auth T] SDF format, chain PA [auth E] SDF format, chain PB [auth U] SDF format, chain QA [auth F] SDF format, chain QB [auth V] SDF format, chain RA [auth G] SDF format, chain RB [auth W] SDF format, chain SA [auth H] MOL2 format, chain AC [auth b] MOL2 format, chain BB [auth L] MOL2 format, chain BC [auth c] MOL2 format, chain CB [auth M] MOL2 format, chain CC [auth d] MOL2 format, chain DB [auth N] MOL2 format, chain EB [auth O] MOL2 format, chain FB [auth P] MOL2 format, chain OA [auth D] MOL2 format, chain OB [auth T] MOL2 format, chain PA [auth E] MOL2 format, chain PB [auth U] MOL2 format, chain QA [auth F] MOL2 format, chain QB [auth V] MOL2 format, chain RA [auth G] MOL2 format, chain RB [auth W] MOL2 format, chain SA [auth H] mmCIF format, chain AC [auth b] mmCIF format, chain BB [auth L] mmCIF format, chain BC [auth c] mmCIF format, chain CB [auth M] mmCIF format, chain CC [auth d] mmCIF format, chain DB [auth N] mmCIF format, chain EB [auth O] mmCIF format, chain FB [auth P] mmCIF format, chain OA [auth D] mmCIF format, chain OB [auth T] mmCIF format, chain PA [auth E] mmCIF format, chain PB [auth U] mmCIF format, chain QA [auth F] mmCIF format, chain QB [auth V] mmCIF format, chain RA [auth G] mmCIF format, chain RB [auth W] mmCIF format, chain SA [auth H]	AC [auth b] BB [auth L] BC [auth c] CB [auth M] CC [auth d] AC [auth b], BB [auth L], BC [auth c], CB [auth M], CC [auth d], DB [auth N], EB [auth O], FB [auth P], OA [auth D], OB [auth T], PA [auth E], PB [auth U], QA [auth F], QB [auth V], RA [auth G], RB [auth W], SA [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AC [auth b] Focus chain BB [auth L] Focus chain BC [auth c] Focus chain CB [auth M] Focus chain CC [auth d] Focus chain DB [auth N] Focus chain EB [auth O] Focus chain FB [auth P] Focus chain OA [auth D] Focus chain OB [auth T] Focus chain PA [auth E] Focus chain PB [auth U] Focus chain QA [auth F] Focus chain QB [auth V] Focus chain RA [auth G] Focus chain RB [auth W] Focus chain SA [auth H] Interactions & Density Focus chain AC [auth b] Focus chain BB [auth L] Focus chain BC [auth c] Focus chain CB [auth M] Focus chain CC [auth d] Focus chain DB [auth N] Focus chain EB [auth O] Focus chain FB [auth P] Focus chain OA [auth D] Focus chain OB [auth T] Focus chain PA [auth E] Focus chain PB [auth U] Focus chain QA [auth F] Focus chain QB [auth V] Focus chain RA [auth G] Focus chain RB [auth W] Focus chain SA [auth H]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AB [auth L] SDF format, chain HA [auth A] SDF format, chain HB [auth Q] SDF format, chain JA [auth B] SDF format, chain JB [auth R] SDF format, chain LA [auth C] SDF format, chain LB [auth S] SDF format, chain NA [auth D] SDF format, chain NB [auth T] SDF format, chain TB [auth Y] SDF format, chain UA [auth I] SDF format, chain VB [auth Z] SDF format, chain WA [auth J] SDF format, chain XB [auth a] SDF format, chain YA [auth K] SDF format, chain ZB [auth b] MOL2 format, chain AB [auth L] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth Q] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth R] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth S] MOL2 format, chain NA [auth D] MOL2 format, chain NB [auth T] MOL2 format, chain TB [auth Y] MOL2 format, chain UA [auth I] MOL2 format, chain VB [auth Z] MOL2 format, chain WA [auth J] MOL2 format, chain XB [auth a] MOL2 format, chain YA [auth K] MOL2 format, chain ZB [auth b] mmCIF format, chain AB [auth L] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth Q] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth R] mmCIF format, chain LA [auth C] mmCIF format, chain LB [auth S] mmCIF format, chain NA [auth D] mmCIF format, chain NB [auth T] mmCIF format, chain TB [auth Y] mmCIF format, chain UA [auth I] mmCIF format, chain VB [auth Z] mmCIF format, chain WA [auth J] mmCIF format, chain XB [auth a] mmCIF format, chain YA [auth K] mmCIF format, chain ZB [auth b]	AB [auth L] HA [auth A] HB [auth Q] JA [auth B] JB [auth R] AB [auth L], HA [auth A], HB [auth Q], JA [auth B], JB [auth R], LA [auth C], LB [auth S], NA [auth D], NB [auth T], TB [auth Y], UA [auth I], VB [auth Z], WA [auth J], XB [auth a], YA [auth K], ZB [auth b]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth L] Focus chain HA [auth A] Focus chain HB [auth Q] Focus chain JA [auth B] Focus chain JB [auth R] Focus chain LA [auth C] Focus chain LB [auth S] Focus chain NA [auth D] Focus chain NB [auth T] Focus chain TB [auth Y] Focus chain UA [auth I] Focus chain VB [auth Z] Focus chain WA [auth J] Focus chain XB [auth a] Focus chain YA [auth K] Focus chain ZB [auth b] Interactions & Density Focus chain AB [auth L] Focus chain HA [auth A] Focus chain HB [auth Q] Focus chain JA [auth B] Focus chain JB [auth R] Focus chain LA [auth C] Focus chain LB [auth S] Focus chain NA [auth D] Focus chain NB [auth T] Focus chain TB [auth Y] Focus chain UA [auth I] Focus chain VB [auth Z] Focus chain WA [auth J] Focus chain XB [auth a] Focus chain YA [auth K] Focus chain ZB [auth b]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.26 Å
R-Value Free: 0.265
R-Value Work: 0.243
R-Value Observed: 0.243
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 435.97	α = 90
b = 183	β = 108.99
c = 225.39	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-05-25

Deposition Author(s):

Cingolani, G.

Duncan, T.M.

Revision History (Full details and data files)

Version 1.0: 2011-05-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description