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- PDB-4f3v: Crystal structure of N-terminal domain of EccA1 ATPase from ESX-1... -

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Basic information

Entry
Database: PDB / ID: 4f3v
TitleCrystal structure of N-terminal domain of EccA1 ATPase from ESX-1 secretion system of Mycobacterium tuberculosis
ComponentsESX-1 secretion system protein EccA1
KeywordsPROTEIN TRANSPORT / tetratricopeptide repeat / TPR domain / ATPase / protein secretion
Function / homology
Function and homology information


biological process involved in interaction with host => GO:0051701 / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Type VII secretion system AAA-ATPase, EccA / CbxX/CfxQ / CbbX, AAA lid domain / AAA lid domain / Tetratricopeptide repeat domain / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily ...Type VII secretion system AAA-ATPase, EccA / CbxX/CfxQ / CbbX, AAA lid domain / AAA lid domain / Tetratricopeptide repeat domain / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
SAMARIUM (III) ION / ESX-1 secretion system protein EccA1 / ESX-1 secretion system protein EccA1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKorotkov, K.V. / Evans, T.J.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of the N-terminal domain of EccA1 ATPase from the ESX-1 secretion system of Mycobacterium tuberculosis.
Authors: Wagner, J.M. / Evans, T.J. / Korotkov, K.V.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: ESX-1 secretion system protein EccA1
B: ESX-1 secretion system protein EccA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,62511
Polymers60,5982
Non-polymers1,0279
Water8,161453
1
A: ESX-1 secretion system protein EccA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8346
Polymers30,2991
Non-polymers5355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ESX-1 secretion system protein EccA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7925
Polymers30,2991
Non-polymers4934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-106 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.230, 92.510, 105.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 0 - 271 / Label seq-ID: 2 - 273

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein ESX-1 secretion system protein EccA1 / ESX conserved component A1 / Type VII secretion system protein EccA1 / T7SS protein EccA1


Mass: 30298.979 Da / Num. of mol.: 2 / Fragment: UNP residues 1-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: eccA1, MT3981, MTV027.03, Rv3868 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O69733, UniProt: P9WPH9*PLUS
#2: Chemical ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Sm
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M SODIUM CITRATE PH 5.6, 1.0M LITHIUM SULFATE, 0.5M AMMONIUM SULFATE, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 49283 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.791 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.63
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.050.7931.55198566843197.9
2.05-2.110.5952.14203466776199.8
2.11-2.170.4472.8197706565199.8
2.17-2.230.3533.47192576378199.8
2.23-2.310.34.12186926206199.6
2.31-2.390.2365.13179795945199.7
2.39-2.480.2075.72176405825199.8
2.48-2.580.1796.65168625554199.9
2.58-2.690.1477.86161645326199.8
2.69-2.830.1219.36155695104199.8
2.83-2.980.09611.29147224830199.7
2.98-3.160.07713.58140114596199.8
3.16-3.380.05917131624324199.7
3.38-3.650.04421.75121063970199.5
3.65-40.03824.63111243658199.3
4-4.470.03328.21101743331199.7
4.47-5.160.03228.6790902971199.7
5.16-6.320.03427.0375232460199.8
6.32-8.940.02832.7858621920199.6
8.94-30.7910.02437.4230721022196.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 6.378 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 2525 5.1 %RANDOM
Rwork0.1738 ---
obs0.1757 49226 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.66 Å2 / Biso mean: 27.3646 Å2 / Biso min: 11.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2---0.47 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 33 453 4621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194249
X-RAY DIFFRACTIONr_bond_other_d0.0040.022784
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9455789
X-RAY DIFFRACTIONr_angle_other_deg1.14936743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3115546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.723.222180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61215645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3541534
X-RAY DIFFRACTIONr_chiral_restr0.070.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214816
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02906
Refine LS restraints NCS

Ens-ID: 1 / Number: 9213 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.13 / Type: LOCAL / Weight: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 171 -
Rwork0.247 3192 -
all-3363 -
obs--100 %
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)
12.06220.7570.08044.34861.03423.4498-0.10050.03030.0624-0.3086-0.01920.2446-0.0095-0.24620.11970.0661-0.0062-0.0310.05990.00120.0326-10.1634.7722.006
21.01370.9748-0.81152.0466-0.91250.7852-0.0136-0.0799-0.0446-0.1909-0.0264-0.10850.02850.03070.040.0840.01110.01410.0456-0.00120.01638.92515.84920.408
31.057-0.0069-0.94532.36721.57213.42970.01810.06850.0127-0.3195-0.0628-0.1015-0.1218-0.06940.04470.15730.05570.10530.03250.03280.086220.96317.920.669
44.5923-2.7616-2.15364.34211.130940.26970.06910.4151-0.4482-0.1955-0.3685-0.261-0.1021-0.07420.18640.03130.06360.01280.01520.07971335.6138.142
541.325623.9727-30.347641.2172-14.495349.40210.7942-0.2158-0.224-1.0659-0.0495-1.814-0.7761.7491-0.74470.16040.04780.10620.1575-0.05290.193117.517-3.25933.281
61.3917-0.24890.47762.9617-0.09822.0280.00870.0283-0.05990.19910.0075-0.16920.0860.0758-0.01620.03490.0141-0.0110.04870.00760.03788.1782.41141.527
71.8801-1.0977-1.64281.01041.34192.64410.08260.1080.0094-0.0676-0.05710.0491-0.0124-0.1077-0.02550.0348-0.00060.00180.061-0.00330.05-12.94116.89448.541
81.20960.2474-1.53192.9507-1.51072.6586-0.0616-0.21450.02790.13190.0762-0.2885-0.12420.2278-0.01460.10250.00040.03380.0604-0.01040.0848-14.90720.05466.765
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 68
2X-RAY DIFFRACTION2A69 - 165
3X-RAY DIFFRACTION3A166 - 250
4X-RAY DIFFRACTION4A251 - 273
5X-RAY DIFFRACTION5B0 - 7
6X-RAY DIFFRACTION6B8 - 78
7X-RAY DIFFRACTION7B79 - 204
8X-RAY DIFFRACTION8B205 - 272

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