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- PDB-3zk2: Crystal structure of the sodium binding rotor ring at pH 8.7 -

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Basic information

Entry
Database: PDB / ID: 3zk2
TitleCrystal structure of the sodium binding rotor ring at pH 8.7
ComponentsATP SYNTHASE SUBUNIT C
KeywordsMEMBRANE PROTEIN / HYDROLASE / ROTOR RING
Function / homology
Function and homology information


proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / identical protein binding / plasma membrane
Similarity search - Function
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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP synthase subunit c
Similarity search - Component
Biological speciesFUSOBACTERIUM NUCLEATUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsSchulz, S. / Meier, T. / Yildiz, O.
CitationJournal: PLoS Biol. / Year: 2013
Title: A new type of Na(+)-driven ATP synthase membrane rotor with a two-carboxylate ion-coupling motif.
Authors: Schulz, S. / Iglesias-Cans, M. / Krah, A. / Yildiz, O. / Leone, V. / Matthies, D. / Cook, G.M. / Faraldo-Gomez, J.D. / Meier, T.
History
DepositionJan 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Structure summary
Revision 2.0Jan 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / database_PDB_caveat / pdbx_validate_chiral
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP SYNTHASE SUBUNIT C
B: ATP SYNTHASE SUBUNIT C
C: ATP SYNTHASE SUBUNIT C
D: ATP SYNTHASE SUBUNIT C
E: ATP SYNTHASE SUBUNIT C
F: ATP SYNTHASE SUBUNIT C
G: ATP SYNTHASE SUBUNIT C
H: ATP SYNTHASE SUBUNIT C
I: ATP SYNTHASE SUBUNIT C
J: ATP SYNTHASE SUBUNIT C
K: ATP SYNTHASE SUBUNIT C
L: ATP SYNTHASE SUBUNIT C
M: ATP SYNTHASE SUBUNIT C
N: ATP SYNTHASE SUBUNIT C
O: ATP SYNTHASE SUBUNIT C
P: ATP SYNTHASE SUBUNIT C
Q: ATP SYNTHASE SUBUNIT C
R: ATP SYNTHASE SUBUNIT C
S: ATP SYNTHASE SUBUNIT C
T: ATP SYNTHASE SUBUNIT C
U: ATP SYNTHASE SUBUNIT C
V: ATP SYNTHASE SUBUNIT C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,71067
Polymers195,10622
Non-polymers11,60545
Water2,108117
1
A: ATP SYNTHASE SUBUNIT C
B: ATP SYNTHASE SUBUNIT C
C: ATP SYNTHASE SUBUNIT C
D: ATP SYNTHASE SUBUNIT C
E: ATP SYNTHASE SUBUNIT C
F: ATP SYNTHASE SUBUNIT C
G: ATP SYNTHASE SUBUNIT C
H: ATP SYNTHASE SUBUNIT C
I: ATP SYNTHASE SUBUNIT C
J: ATP SYNTHASE SUBUNIT C
K: ATP SYNTHASE SUBUNIT C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,59634
Polymers97,55311
Non-polymers6,04423
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55050 Å2
ΔGint-501.2 kcal/mol
Surface area34950 Å2
MethodPISA
2
L: ATP SYNTHASE SUBUNIT C
M: ATP SYNTHASE SUBUNIT C
N: ATP SYNTHASE SUBUNIT C
O: ATP SYNTHASE SUBUNIT C
P: ATP SYNTHASE SUBUNIT C
Q: ATP SYNTHASE SUBUNIT C
R: ATP SYNTHASE SUBUNIT C
S: ATP SYNTHASE SUBUNIT C
T: ATP SYNTHASE SUBUNIT C
U: ATP SYNTHASE SUBUNIT C
V: ATP SYNTHASE SUBUNIT C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,11433
Polymers97,55311
Non-polymers5,56122
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53080 Å2
ΔGint-527.7 kcal/mol
Surface area34410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.770, 83.900, 150.990
Angle α, β, γ (deg.)90.00, 112.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
ATP SYNTHASE SUBUNIT C / / ATP SYNTHASE F(0) SECTOR SUBUNIT C / F-TYPE ATPASE SUBUNIT C / F-ATPASE SUBUNIT C / LIPID-BINDING PROTEIN


Mass: 8868.433 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FUSOBACTERIUM NUCLEATUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DK8 / References: UniProt: Q8RGD7
#2: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Na
#3: Sugar...
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 23
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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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: 4.13 Å3/Da / Density % sol: 0.7 % / Description: NONE
Crystal growpH: 8.7 / Details: pH 8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.64→20 Å / Num. obs: 92330 / % possible obs: 98.3 % / Observed criterion σ(I): 1.6 / Redundancy: 4.2 % / Biso Wilson estimate: 36.92 Å2 / Rmerge(I) obs: 0.28 / Net I/σ(I): 6.99
Reflection shellResolution: 2.64→2.8 Å / Redundancy: 3.96 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 1.57 / % possible all: 90.8

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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 3ZK1

3zk1


Resolution: 2.63→46.998 Å / SU ML: 0.42 / σ(F): 1.99 / Phase error: 31.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2974 4605 5 %
Rwork0.2554 --
obs0.2575 92184 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→46.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13639 0 781 117 14537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02114553
X-RAY DIFFRACTIONf_angle_d2.33319689
X-RAY DIFFRACTIONf_dihedral_angle_d12.545481
X-RAY DIFFRACTIONf_chiral_restr0.1142584
X-RAY DIFFRACTIONf_plane_restr0.0032331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6296-2.65950.3331110.32862117X-RAY DIFFRACTION72
2.6595-2.69080.41611590.31892826X-RAY DIFFRACTION97
2.6908-2.72360.35591430.31012962X-RAY DIFFRACTION100
2.7236-2.75810.32541570.30132916X-RAY DIFFRACTION100
2.7581-2.79440.33651530.29352968X-RAY DIFFRACTION100
2.7944-2.83260.3471500.29382888X-RAY DIFFRACTION100
2.8326-2.87310.30491610.28642944X-RAY DIFFRACTION100
2.8731-2.9160.37051490.28912936X-RAY DIFFRACTION100
2.916-2.96150.361580.28272957X-RAY DIFFRACTION100
2.9615-3.01010.31851570.28012957X-RAY DIFFRACTION100
3.0101-3.0620.31861500.27412877X-RAY DIFFRACTION100
3.062-3.11760.31371580.27872964X-RAY DIFFRACTION100
3.1176-3.17760.33841570.27022919X-RAY DIFFRACTION100
3.1776-3.24240.31461510.26272969X-RAY DIFFRACTION100
3.2424-3.31290.30221550.25892948X-RAY DIFFRACTION100
3.3129-3.390.31881550.25752949X-RAY DIFFRACTION100
3.39-3.47470.28861600.24962964X-RAY DIFFRACTION100
3.4747-3.56860.32321490.24892914X-RAY DIFFRACTION100
3.5686-3.67360.29141600.23712980X-RAY DIFFRACTION100
3.6736-3.79210.31061530.24432943X-RAY DIFFRACTION100
3.7921-3.92760.25781540.24632921X-RAY DIFFRACTION100
3.9276-4.08480.26891570.23512983X-RAY DIFFRACTION100
4.0848-4.27060.26311560.25392934X-RAY DIFFRACTION100
4.2706-4.49550.26311540.24352956X-RAY DIFFRACTION100
4.4955-4.7770.32531560.2482966X-RAY DIFFRACTION100
4.777-5.14540.2881530.24552998X-RAY DIFFRACTION100
5.1454-5.66240.29891600.24522962X-RAY DIFFRACTION100
5.6624-6.47990.2581570.23122996X-RAY DIFFRACTION100
6.4799-8.15710.19961570.19862992X-RAY DIFFRACTION100
8.1571-47.00510.30891550.24722973X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 53.4786 Å / Origin y: 0.7787 Å / Origin z: 34.7399 Å
111213212223313233
T0.1464 Å2-0.0107 Å2-0.0615 Å2-0.2079 Å20.023 Å2--0.2802 Å2
L0.0802 °20.011 °20.2259 °2-0.1113 °20.0113 °2--1.1843 °2
S0.0033 Å °-0.0235 Å °0.006 Å °0.0028 Å °-0.014 Å °-0.0147 Å °0.0276 Å °0.0657 Å °-0.0136 Å °
Refinement TLS groupSelection details: ALL

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