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- PDB-5zt1: Structure of the bacterial pathogens ATPase with substrate ATP gamma S -

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Basic information

Entry
Database: PDB / ID: 5zt1
TitleStructure of the bacterial pathogens ATPase with substrate ATP gamma S
ComponentsProbable ATP synthase SpaL/MxiB
KeywordsHYDROLASE / ATPase / T3SS / hexamer / ATP gamma S
Function / homology
Function and homology information


protein-exporting ATPase activity / protein-secreting ATPase / type III protein secretion system complex / protein secretion by the type III secretion system / biosynthetic process / ATP metabolic process / proton transmembrane transport / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / 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 / ATPases associated with a variety of cellular activities ...ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Type 3 secretion system ATPase
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.114 Å
AuthorsGao, X.P. / Mu, Z.X. / Cui, S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81572005 China
National Natural Science Foundation of China81401714 China
CitationJournal: Front Microbiol / Year: 2018
Title: Structural Insight Into Conformational Changes Induced by ATP Binding in a Type III Secretion-Associated ATPase FromShigella flexneri
Authors: Gao, X. / Mu, Z. / Yu, X. / Qin, B. / Wojdyla, J. / Wang, M. / Cui, S.
History
DepositionMay 1, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 16, 2018ID: 5WX0
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Probable ATP synthase SpaL/MxiB
A: Probable ATP synthase SpaL/MxiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,78334
Polymers82,3632
Non-polymers1,42032
Water0
1
B: Probable ATP synthase SpaL/MxiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,81121
Polymers41,1821
Non-polymers63020
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-15 kcal/mol
Surface area15370 Å2
MethodPISA
2
A: Probable ATP synthase SpaL/MxiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,97213
Polymers41,1821
Non-polymers79112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.267, 104.267, 145.769
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Probable ATP synthase SpaL/MxiB


Mass: 41181.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: spaL, mxiB, spa47, CP0149 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: P0A1C1, H+-transporting two-sector ATPase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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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: 2.67 Å3/Da / Density meas: 0.01 Mg/m3 / Density % sol: 54 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 0.1M Bicine pH8.6;1.2M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97876 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2013
RadiationMonochromator: Double Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 16927 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.43 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 17.78
Reflection shellResolution: 3.11→3.3 Å / Redundancy: 8.86 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 5.23 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2obl

2obl


Resolution: 3.114→29.868 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.78
Details: Authors state that the low occupancy of the ligands result from only fewer protein molecules bound ligands.we balanced B-factors and occupancy of ligands when refinement. SF FILE CONTAINS ...Details: Authors state that the low occupancy of the ligands result from only fewer protein molecules bound ligands.we balanced B-factors and occupancy of ligands when refinement. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2546 3127 9.92 %
Rwork0.1915 --
obs0.1977 16820 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.114→29.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5205 0 70 0 5275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0175345
X-RAY DIFFRACTIONf_angle_d1.4667228
X-RAY DIFFRACTIONf_dihedral_angle_d13.7713226
X-RAY DIFFRACTIONf_chiral_restr0.065826
X-RAY DIFFRACTIONf_plane_restr0.008925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1136-3.16220.3481320.33011148X-RAY DIFFRACTION87
3.1622-3.2140.35431420.22921289X-RAY DIFFRACTION100
3.214-3.26940.33791400.23361302X-RAY DIFFRACTION100
3.2694-3.32870.29761360.23981290X-RAY DIFFRACTION100
3.3287-3.39270.31681460.22661317X-RAY DIFFRACTION100
3.3927-3.46180.2681420.20451304X-RAY DIFFRACTION100
3.4618-3.5370.32281480.19881288X-RAY DIFFRACTION100
3.537-3.61910.29211420.18171285X-RAY DIFFRACTION100
3.6191-3.70950.27561420.18571288X-RAY DIFFRACTION100
3.7095-3.80960.23741480.18791325X-RAY DIFFRACTION100
3.8096-3.92140.25421320.18671288X-RAY DIFFRACTION100
3.9214-4.04770.25111500.1821297X-RAY DIFFRACTION100
4.0477-4.1920.23961430.18191292X-RAY DIFFRACTION100
4.192-4.35940.23641280.16871319X-RAY DIFFRACTION100
4.3594-4.55710.21931530.15721277X-RAY DIFFRACTION100
4.5571-4.79650.17761460.15731301X-RAY DIFFRACTION100
4.7965-5.09560.23121460.16721304X-RAY DIFFRACTION100
5.0956-5.48680.25451380.16981316X-RAY DIFFRACTION100
5.4868-6.03480.25691400.18851286X-RAY DIFFRACTION100
6.0348-6.89870.2361440.20081320X-RAY DIFFRACTION100
6.8987-8.65640.20341450.1811288X-RAY DIFFRACTION100
8.6564-29.86980.24421440.20141286X-RAY DIFFRACTION100

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