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- PDB-6pi4: Crystal structure of ATP synthase epsion chain ATP synthase epsil... -

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Basic information

Entry
Database: PDB / ID: 6pi4
TitleCrystal structure of ATP synthase epsion chain ATP synthase epsilon chain (ATP synthase F1 sector epsilon subunit) (F-ATPase epsilon subunit) from Mycobacterium smegmatis
ComponentsATP synthase epsilon chain
KeywordsPROTEIN TRANSPORT / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain
Similarity search - Domain/homology
CACODYLATE ION / ATP synthase epsilon chain
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of ATP synthase epsion chain ATP synthase epsilon chain (ATP synthase F1 sector epsilon subunit) (F-ATPase epsilon subunit) from Mycobacterium smegmatis
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJun 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4462
Polymers14,3091
Non-polymers1371
Water46826
1
A: ATP synthase epsilon chain
hetero molecules

A: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8924
Polymers28,6182
Non-polymers2742
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3890 Å2
ΔGint-15 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.870, 75.320, 71.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

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Components

#1: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 14308.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: atpC, MSMEG_4935, MSMEI_4808 / Plasmid: MysmA.18337.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: A0R1Z9
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: RigakuReagents JCSG+ screen, B10: 50% PEG 200, 200mM MgCl2, 100mM sodium cacodylate pH 6.5: MysmA.18337.a.B1.PS38196 at 17.3mg/ml + 6mM MgCl2 + 6mM ATP. Cryo: direct: tray 290121 B10: puck nww5-5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 9, 2017
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→43.817 Å / Num. obs: 8662 / % possible obs: 99.1 % / Redundancy: 6.101 % / Biso Wilson estimate: 48.139 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.059 / Χ2: 1.01 / Net I/σ(I): 17.28 / Num. measured all: 52850 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.156.2250.5383.4839286386310.9590.58798.9
2.15-2.216.1920.493.7737966136130.9520.534100
2.21-2.286.2830.4234.3137516055970.9510.46298.7
2.28-2.356.1910.2855.8636035885820.9840.31199
2.35-2.426.1880.2666.135215705690.9860.29199.8
2.42-2.516.2120.2237.2232555295240.9890.24299.1
2.51-2.66.1460.1968.0232885375350.9890.21499.6
2.6-2.716.1250.1479.932225305260.9950.1699.2
2.71-2.836.2270.11812.8129894824800.9960.12899.6
2.83-2.976.0480.08515.9628734764750.9980.09299.8
2.97-3.136.090.06621.1727164484460.9980.07299.6
3.13-3.326.0140.04926.0726104374340.9990.05499.3
3.32-3.556.060.04230.5924244024000.9990.04699.5
3.55-3.836.0320.03635.3922383753710.9990.0498.9
3.83-4.25.980.03637.1120633483450.9990.0499.1
4.2-4.75.9620.03242.3218903193170.9990.03599.4
4.7-5.425.9040.03244.216652842820.9990.03599.3
5.42-6.645.820.03142.5413912422390.9990.03498.8
6.64-9.395.6070.02945.1310711971910.9980.03297
9.39-43.8175.2950.02749.055561181050.9970.0389

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3500)refinement
PDB_EXTRACT3.25data extraction
MR-Rosettaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MR-Rosetta using top 8 hhm hits: 6FOC_H, 1FS0_E, 6FKF_E, 5IK2_P, 5DN6_I, 5ZWL_E, 2E5Y_H, 6F5D_H

Resolution: 2.1→43.817 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.97
RfactorNum. reflection% reflectionSelection details
Rfree0.2831 862 9.99 %0
Rwork0.22 ---
obs0.2261 8631 98.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 168.09 Å2 / Biso mean: 70.012 Å2 / Biso min: 32.94 Å2
Refinement stepCycle: final / Resolution: 2.1→43.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms876 0 5 26 907
Biso mean--144.4 58.46 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007891
X-RAY DIFFRACTIONf_angle_d0.8061217
X-RAY DIFFRACTIONf_dihedral_angle_d17.593530
X-RAY DIFFRACTIONf_chiral_restr0.055147
X-RAY DIFFRACTIONf_plane_restr0.005163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.23160.39541600.33661274143499
2.2316-2.40390.3841560.29521233138999
2.4039-2.64580.3381190.28361300141999
2.6458-3.02850.29511340.25111300143499
3.0285-3.81530.26581500.21641301145199
3.8153-43.82610.24891430.17851361150498
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.3042-0.70571.91162.268-2.14832.31290.12860.4919-0.7735-0.38910.14570.30161.1563-0.5832-0.39250.3855-0.0913-0.00160.4748-0.02440.437727.910514.68355.3145
25.76190.8235-0.33113.8422.29697.8534-0.0441-0.89480.13510.1203-0.0414-0.0549-0.05860.41780.02960.32350.0112-0.00460.5435-0.00750.319219.08218.08935.0354
36.9101-0.49080.52514.13831.23788.1316-0.1781-0.5791-0.19740.1770.0067-0.01890.2501-0.36690.13650.31710.01840.05120.5619-0.09920.41815.403616.877433.9687
47.9069-0.14812.04184.26821.91328.12-0.1605-1.0138-0.04280.1320.2511-0.1896-0.5435-0.2179-0.16980.31510.03540.00640.4234-0.0790.434321.805321.926334.4107
57.8912-0.71950.67782.8442-1.06133.67330.04150.28350.58250.6422-0.281-0.3524-0.6267-0.04080.28840.536-0.0612-0.06530.4315-0.0180.434122.996221.357628.2856
68.2709-4.62434.35773.8983-3.92283.97341.511.82740.60270.1523-0.30790.65430.7714-0.4378-1.33251.64360.3494-0.09770.89790.15281.247712.517436.970821.6753
79.11593.2671.75035.89411.72524.287-0.3607-0.85371.29060.3519-0.55770.9319-2.6017-1.8180.79561.17730.3757-0.04430.7154-0.2010.703213.067831.254627.4578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 12 )A3 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 35 )A13 - 35
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 54 )A36 - 54
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 72 )A55 - 72
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 91 )A73 - 91
6X-RAY DIFFRACTION6chain 'A' and (resid 92 through 103 )A92 - 103
7X-RAY DIFFRACTION7chain 'A' and (resid 104 through 121 )A104 - 121

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