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- PDB-4bem: Crystal structure of the F-type ATP synthase c-ring from Acetobac... -

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Basic information

Entry
Database: PDB / ID: 4bem
TitleCrystal structure of the F-type ATP synthase c-ring from Acetobacterium woodii.
Components
  • F1FO ATPASE C1 SUBUNIT
  • F1FO ATPASE C2 SUBUNIT
KeywordsHYDROLASE
Function / homology
Function and homology information


proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / hydrolase activity / lipid binding / metal ion binding / plasma membrane
Similarity search - Function
lithium bound rotor ring of v- atpase / F1F0 ATP synthase subunit C / F1FO ATP Synthase / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C ...lithium bound rotor ring of v- atpase / F1F0 ATP synthase subunit C / F1FO ATP Synthase / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / : / ATP synthase subunit c / ATP synthase subunit c / ATP synthase subunit c / ATP synthase subunit c
Similarity search - Component
Biological speciesACETOBACTERIUM WOODII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMatthies, D. / Meier, T. / Yildiz, O.
CitationJournal: Nat.Commun. / Year: 2014
Title: High-Resolution Structure and Mechanism of an F/V-Hybrid Rotor Ring in a Na+-Coupled ATP Synthase
Authors: Matthies, D. / Zhou, W. / Klyszejko, A.L. / Anselmi, C. / Yildiz, O. / Brandt, K. / Muller, V. / Faraldo-Gomez, J.D. / Meier, T.
History
DepositionMar 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F1FO ATPASE C2 SUBUNIT
B: F1FO ATPASE C2 SUBUNIT
C: F1FO ATPASE C2 SUBUNIT
D: F1FO ATPASE C2 SUBUNIT
E: F1FO ATPASE C2 SUBUNIT
F: F1FO ATPASE C2 SUBUNIT
G: F1FO ATPASE C2 SUBUNIT
H: F1FO ATPASE C2 SUBUNIT
I: F1FO ATPASE C2 SUBUNIT
J: F1FO ATPASE C1 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,89646
Polymers92,33610
Non-polymers6,56036
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46220 Å2
ΔGint-493.4 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.170, 121.170, 150.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 2 types, 10 molecules ABCDEFGHIJ

#1: Protein
F1FO ATPASE C2 SUBUNIT / F1FO ATPASE C3 SUBUNIT


Mass: 8213.572 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) ACETOBACTERIUM WOODII (bacteria) / Strain: DSM 1030 / References: UniProt: Q59166, UniProt: H6LFT2*PLUS
#2: Protein F1FO ATPASE C1 SUBUNIT


Mass: 18413.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ACETOBACTERIUM WOODII (bacteria) / Strain: DSM 1030 / References: UniProt: Q9RMB5, UniProt: H6LFT0*PLUS

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Sugars , 1 types, 19 molecules

#4: Sugar
ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM

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Non-polymers , 6 types, 181 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 0.6 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 65395 / % possible obs: 99.3 % / Observed criterion σ(I): 1.6 / Redundancy: 16.6 % / Biso Wilson estimate: 37.21 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 18.08
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 16.5 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 1.58 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YCE

1yce


Resolution: 2.1→47.2 Å / SU ML: 0.21 / σ(F): 1.99 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 3270 5 %
Rwork0.1818 --
obs0.1837 65363 99.22 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6474 0 415 164 7053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076964
X-RAY DIFFRACTIONf_angle_d0.9369361
X-RAY DIFFRACTIONf_dihedral_angle_d16.4222578
X-RAY DIFFRACTIONf_chiral_restr0.0591140
X-RAY DIFFRACTIONf_plane_restr0.0041155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0999-2.13130.3251390.27762643X-RAY DIFFRACTION99
2.1313-2.16460.31151390.25772652X-RAY DIFFRACTION99
2.1646-2.20010.29291390.23762640X-RAY DIFFRACTION99
2.2001-2.2380.27971400.2212651X-RAY DIFFRACTION99
2.238-2.27870.23381400.21142660X-RAY DIFFRACTION99
2.2787-2.32250.24731390.22633X-RAY DIFFRACTION99
2.3225-2.36990.26771400.19472665X-RAY DIFFRACTION99
2.3699-2.42150.22941410.18732679X-RAY DIFFRACTION99
2.4215-2.47780.22431400.16572673X-RAY DIFFRACTION99
2.4778-2.53980.22771400.16472647X-RAY DIFFRACTION99
2.5398-2.60840.1921400.14812671X-RAY DIFFRACTION99
2.6084-2.68520.22381430.16592708X-RAY DIFFRACTION99
2.6852-2.77180.18611400.15252668X-RAY DIFFRACTION99
2.7718-2.87090.17941420.13892686X-RAY DIFFRACTION99
2.8709-2.98580.17531420.14562695X-RAY DIFFRACTION99
2.9858-3.12170.19141430.16052721X-RAY DIFFRACTION100
3.1217-3.28620.20261420.15952701X-RAY DIFFRACTION99
3.2862-3.49210.20331430.15992724X-RAY DIFFRACTION100
3.4921-3.76160.21491440.16292729X-RAY DIFFRACTION100
3.7616-4.13990.19921450.15562751X-RAY DIFFRACTION100
4.1399-4.73850.22451460.16982773X-RAY DIFFRACTION100
4.7385-5.96810.2081480.21532803X-RAY DIFFRACTION100
5.9681-47.21150.24941550.22772920X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 24.4461 Å / Origin y: 23.5329 Å / Origin z: 36.7719 Å
111213212223313233
T0.2967 Å2-0.0406 Å20.0169 Å2-0.3221 Å20.0268 Å2--0.2933 Å2
L2.3368 °21.1926 °2-0.3656 °2-2.1647 °2-0.4106 °2--1.2201 °2
S0.1477 Å °-0.0972 Å °0.3247 Å °0.2862 Å °-0.1489 Å °0.0644 Å °-0.153 Å °0.2203 Å °0.0029 Å °
Refinement TLS groupSelection details: ALL

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