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- PDB-6tv1: ATPase domain D3 of the EssC coupling protein from S. aureus USA300 -

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Basic information

Entry
Database: PDB / ID: 6tv1
TitleATPase domain D3 of the EssC coupling protein from S. aureus USA300
ComponentsEssC protein
KeywordsPROTEIN BINDING / ATPase Domain
Function / homology
Function and homology information


: / membrane => GO:0016020 / DNA binding / ATP binding / plasma membrane
Similarity search - Function
Firmicutes EssC, N-terminal / Firmicutes EssC, C-terminal / DNA transporter / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / SMAD/FHA domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type VII secretion system protein EssC
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsMietrach, N.A. / Geibel, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Elite Network of BavariaN-BM-2013-246 Germany
CitationJournal: J.Bacteriol. / Year: 2020
Title: Substrate Interaction with the EssC Coupling Protein of the Type VIIb Secretion System.
Authors: Mietrach, N. / Damian-Aparicio, D. / Mielich-Suss, B. / Lopez, D. / Geibel, S.
History
DepositionJan 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EssC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2902
Polymers27,1981
Non-polymers921
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.030, 91.030, 124.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1693-

HOH

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Components

#1: Protein EssC protein


Mass: 27198.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300 (bacteria)
Gene: SAUSA300_0283 / Plasmid: pet16b(+) / Production host: Escherichia coli (E. coli) / Variant (production host): Bl21 star / References: UniProt: A0A0H2XEV3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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

CrystalDescription: octahedral
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1,4-1,8 M ammonium citrate / PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2016
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→19.751 Å / Num. obs: 57937 / % possible obs: 99.66 % / Redundancy: 8.7 % / CC1/2: 1 / Rmerge(I) obs: 0.04526 / Rpim(I) all: 0.01575 / Rrim(I) all: 0.04807 / Net I/σ(I): 25.71
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.559 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 4176 / CC1/2: 0.539 / Rpim(I) all: 0.5333 / Rrim(I) all: 1.743 / % possible all: 98.72

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata scaling
PHENIX1.15.2_3472phasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.751 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.95
RfactorNum. reflection% reflection
Rfree0.1724 2897 5 %
Rwork0.1528 --
obs0.1538 57937 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.2 Å2 / Biso mean: 38.5522 Å2 / Biso min: 21.79 Å2
Refinement stepCycle: final / Resolution: 1.7→19.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 0 6 97 1963
Biso mean--45.94 48.76 -
Num. residues----228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7002-1.72810.36341330.3389251197
1.7281-1.75790.31751370.27822604100
1.7579-1.78980.26081360.24212583100
1.7898-1.82420.24631360.19742584100
1.8242-1.86140.21221350.18012579100
1.8614-1.90190.19831380.16012608100
1.9019-1.94610.20021350.14512579100
1.9461-1.99470.16611360.13752574100
1.9947-2.04860.1621360.1342593100
2.0486-2.10880.16141380.12962623100
2.1088-2.17680.14741370.10882603100
2.1768-2.25450.15071370.10872600100
2.2545-2.34460.13291390.10952629100
2.3446-2.45110.15641370.12312614100
2.4511-2.58010.19191370.13852611100
2.5801-2.74130.16411380.14672637100
2.7413-2.95240.16821400.14942643100
2.9524-3.24830.17551390.1522652100
3.2483-3.71560.15561400.14652655100
3.7156-4.6710.16951430.14192717100
4.671-19.7510.17551500.1937284199

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