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- PDB-4n1a: Thermomonospora curvata EccC (ATPases 2 and 3) in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 4n1a
TitleThermomonospora curvata EccC (ATPases 2 and 3) in complex with a signal sequence peptide
Components
  • Cell divisionFtsK/SpoIIIE
  • Uncharacterized protein
KeywordsPROTEIN BINDING/PROTEIN BINDING / ATPase / PROTEIN BINDING-PROTEIN BINDING complex
Function / homology
Function and homology information


localization / ATP hydrolysis activity / DNA binding / extracellular region / ATP binding / plasma membrane
Similarity search - Function
ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities ...ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ESX secretion system protein EccC / ESAT-6-like protein
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsDovala, D.L. / Bendebury, A. / Cox, J.S. / Stroud, R.M. / Rosenberg, O.S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2015
Title: Substrates Control Multimerization and Activation of the Multi-Domain ATPase Motor of Type VII Secretion.
Authors: Rosenberg, O.S. / Dovala, D. / Li, X. / Connolly, L. / Bendebury, A. / Finer-Moore, J. / Holton, J. / Cheng, Y. / Stroud, R.M. / Cox, J.S.
History
DepositionOct 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _struct_conn.ptnr2_label_asym_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: Cell divisionFtsK/SpoIIIE
B: Cell divisionFtsK/SpoIIIE
C: Cell divisionFtsK/SpoIIIE
G: Uncharacterized protein
H: Uncharacterized protein
J: Uncharacterized protein
E: Cell divisionFtsK/SpoIIIE
K: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,73322
Polymers269,4958
Non-polymers3,23814
Water181
1
A: Cell divisionFtsK/SpoIIIE
G: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4376
Polymers67,3742
Non-polymers1,0634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell divisionFtsK/SpoIIIE
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4376
Polymers67,3742
Non-polymers1,0634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Cell divisionFtsK/SpoIIIE
K: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4224
Polymers67,3742
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Cell divisionFtsK/SpoIIIE
J: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4376
Polymers67,3742
Non-polymers1,0634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)216.150, 216.150, 186.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Cell divisionFtsK/SpoIIIE


Mass: 64810.992 Da / Num. of mol.: 4 / Fragment: UNP residues 753-1315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (bacteria) / Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NCIMB 10081 / Gene: Tcur_0607 / Production host: Escherichia coli (E. coli) / References: UniProt: D1A4G7
#2: Protein/peptide
Uncharacterized protein


Mass: 2562.790 Da / Num. of mol.: 4 / Fragment: UNP residues 82-104 / Source method: obtained synthetically / Source: (synth.) Thermomonospora curvata (bacteria) / References: UniProt: D1A4H0
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.03 Å3/Da / Density % sol: 69.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: Citric Acid, pH 5.2, 1.28M LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2013
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.24→152.6 Å / Num. obs: 85798

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.24→49.15 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 -Random
Rwork0.2262 --
obs-85798 -
Refinement stepCycle: LAST / Resolution: 3.24→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17265 0 194 1 17460

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