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Basic information

Entry
Database: PDB / ID: 2obm
TitleStructural and biochemical analysis of a prototypical ATPase from the type III secretion system of pathogenic bacteria
ComponentsEscN
KeywordsHYDROLASE / ATPase
Function / homology
Function and homology information


protein-secreting ATPase / type III protein secretion system complex / protein secretion by the type III secretion system / : / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #330 / Type 3 secretion system ATPase SCTN / ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / : / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #330 / Type 3 secretion system ATPase SCTN / ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / : / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / protein-secreting ATPase / protein-secreting ATPase
Similarity search - Component
Biological speciesEscherichia coli O127:H6 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsZarivach, R. / Vuckovic, M. / Deng, W. / Finlay, B.B. / Strynadka, N.C.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structural analysis of a prototypical ATPase from the type III secretion system.
Authors: Zarivach, R. / Vuckovic, M. / Deng, W. / Finlay, B.B. / Strynadka, N.C.
History
DepositionDec 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN AMP-PNP was used for crystallization setup which may be hydrolyzed to ADP

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EscN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1353
Polymers37,6671
Non-polymers4672
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.131, 78.690, 53.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1001-

CA

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Components

#1: Protein EscN


Mass: 37667.402 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, residues 103-446 / Mutation: V393P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (bacteria) / Species: Escherichia coli / Strain: E2348/69 / Gene: escN / Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O52140, UniProt: B7UMA6*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 7% (w/v) PEG 8000, 0.1M Calcium Acetate, 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5428 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5428 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 17405 / Num. obs: 17196 / % possible obs: 98.8 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.3
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 5.23 / Num. unique all: 1704 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OBL

1obl


Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.517 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.354 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26329 867 5.1 %RANDOM
Rwork0.20817 ---
obs0.21088 16271 98.76 %-
all-16475 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.775 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20 Å2
2---0.51 Å20 Å2
3---1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 28 133 2756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222708
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1812.0053678
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5535349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77823.571112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19615480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7921524
X-RAY DIFFRACTIONr_chiral_restr0.0770.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022014
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.31155
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.51850
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.5272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.51
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.342
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2830.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0430.51
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.98221759
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64332765
X-RAY DIFFRACTIONr_scbond_it0.87121049
X-RAY DIFFRACTIONr_scangle_it1.3813908
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.247→2.305 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 69 -
Rwork0.23 1155 -
obs-1155 96 %

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