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- PDB-5ybi: Structure of the bacterial pathogens ATPase with substrate AMPPNP -

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Basic information

Entry
Database: PDB / ID: 5ybi
TitleStructure of the bacterial pathogens ATPase with substrate AMPPNP
ComponentsProbable ATP synthase SpaL/MxiB
KeywordsHYDROLASE / ATPase / T3SS / hexamer / AMPPNP
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 / proton-transporting ATP synthase activity, rotational mechanism / 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 ...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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Type 3 secretion system ATPase
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.268 Å
AuthorsMu, Z.X. / Gao, X.P. / Cui, S.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China81572005 China
National Natural Science Foundation of China81401714 China
Beijing Natural Science Foundation7154226 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
DepositionSep 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 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.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.name
Revision 1.2Dec 18, 2019Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 22, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / 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.ptnr1_symmetry / _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.ptnr2_symmetry / _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.ptnr3_symmetry / _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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,46648
Polymers82,3632
Non-polymers2,10246
Water6,287349
1
A: Probable ATP synthase SpaL/MxiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,46122
Polymers41,1821
Non-polymers1,27921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-16 kcal/mol
Surface area15380 Å2
MethodPISA
2
B: Probable ATP synthase SpaL/MxiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,00526
Polymers41,1821
Non-polymers82325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.017, 105.017, 146.642
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 / Fragment: UNP residues 84-430
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


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.72 Å3/Da / Density meas: 0.01 Mg/m3 / Density % sol: 54.9 %
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: BL17B1 / 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: 2.2→43.4 Å / Num. obs: 82611 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.52 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.56
Reflection shellResolution: 2.2→2.41 Å / Redundancy: 8.44 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.27 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YBH

5ybh


Resolution: 2.268→43 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.48
RfactorNum. reflection% reflection
Rfree0.227 4138 5.01 %
Rwork0.1794 --
obs0.1818 82596 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.268→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5327 0 104 349 5780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015538
X-RAY DIFFRACTIONf_angle_d1.1497499
X-RAY DIFFRACTIONf_dihedral_angle_d14.8252067
X-RAY DIFFRACTIONf_chiral_restr0.045848
X-RAY DIFFRACTIONf_plane_restr0.006965
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.268-2.2940.30461420.27632537X-RAY DIFFRACTION94
2.294-2.3210.30391520.23812616X-RAY DIFFRACTION100
2.321-2.34930.2951390.23242635X-RAY DIFFRACTION100
2.3493-2.3790.26451270.21822743X-RAY DIFFRACTION100
2.379-2.41030.21681330.21312544X-RAY DIFFRACTION100
2.4103-2.44330.29191350.21062775X-RAY DIFFRACTION100
2.4433-2.47820.24051300.20842612X-RAY DIFFRACTION100
2.4782-2.51520.25911310.20412675X-RAY DIFFRACTION100
2.5152-2.55450.22111290.19672656X-RAY DIFFRACTION100
2.5545-2.59640.23921210.19192686X-RAY DIFFRACTION100
2.5964-2.64120.25691400.18812625X-RAY DIFFRACTION100
2.6412-2.68920.21381520.19572669X-RAY DIFFRACTION100
2.6892-2.74090.29821400.19912617X-RAY DIFFRACTION100
2.7409-2.79680.22041650.1922613X-RAY DIFFRACTION100
2.7968-2.85760.29741400.19922675X-RAY DIFFRACTION100
2.8576-2.92410.31951430.19482690X-RAY DIFFRACTION100
2.9241-2.99720.28021420.20652641X-RAY DIFFRACTION100
2.9972-3.07820.24331320.19542646X-RAY DIFFRACTION100
3.0782-3.16880.25711440.19122623X-RAY DIFFRACTION100
3.1688-3.2710.24471550.18722655X-RAY DIFFRACTION100
3.271-3.38790.25611400.19212677X-RAY DIFFRACTION100
3.3879-3.52350.24571480.17752626X-RAY DIFFRACTION100
3.5235-3.68370.2365890.18561910X-RAY DIFFRACTION99
3.6837-3.87780.20631090.15942450X-RAY DIFFRACTION99
3.8778-4.12060.18691780.14582592X-RAY DIFFRACTION100
4.1206-4.43850.16671600.13922616X-RAY DIFFRACTION100
4.4385-4.88460.15611230.12792682X-RAY DIFFRACTION100
4.8846-5.59020.17011440.15322656X-RAY DIFFRACTION100
5.5902-7.03820.23171450.18492639X-RAY DIFFRACTION100
7.0382-43.44120.19971100.16992677X-RAY DIFFRACTION99

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