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- PDB-6h17: Myxococcus xanthus MglA bound to GTPgammaS -

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Basic information

Entry
Database: PDB / ID: 6h17
TitleMyxococcus xanthus MglA bound to GTPgammaS
ComponentsMutual gliding-motility protein MglA
KeywordsCYTOSOLIC PROTEIN / GTPase / motility
Function / homology
Function and homology information


regulation of protein localization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Mutual gliding-motility protein MglA
Similarity search - Component
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.275 Å
AuthorsGalicia, C. / Cherfils, J.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Nat Commun / Year: 2019
Title: MglA functions as a three-state GTPase to control movement reversals of Myxococcus xanthus.
Authors: Galicia, C. / Lhospice, S. / Varela, P.F. / Trapani, S. / Zhang, W. / Navaza, J. / Herrou, J. / Mignot, T. / Cherfils, J.
History
DepositionJul 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 11, 2020Group: Derived calculations / Refinement description / Structure summary
Category: pdbx_struct_conn_angle / software ...pdbx_struct_conn_angle / software / struct / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.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.value / _software.name / _struct.title / _struct_conn.pdbx_dist_value / _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
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Mutual gliding-motility protein MglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6275
Polymers22,8711
Non-polymers7564
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-39 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.349, 117.349, 117.349
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-646-

HOH

21A-706-

HOH

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Components

#1: Protein Mutual gliding-motility protein MglA


Mass: 22871.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Mg and GTPgS bound / Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Gene: mglA, MXAN_1925 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1DB04
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.94 Å3/Da / Density % sol: 58.22 % / Description: cube
Crystal growTemperature: 277 K / Method: microbatch / pH: 4.6
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate, 12% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980073 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980073 Å / Relative weight: 1
ReflectionResolution: 1.275→47.91 Å / Num. obs: 67069 / % possible obs: 96 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06168 / Rpim(I) all: 0.02533 / Rrim(I) all: 0.067 / Net I/σ(I): 14
Reflection shellResolution: 1.275→1.32 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.43 / Num. unique obs: 4993 / CC1/2: 0.623 / Rpim(I) all: 0.469 / % possible all: 63.23

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.275→47.91 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1627 --
Rwork0.1471 --
obs-67060 99 %
Displacement parametersBiso mean: 22.17 Å2
Refinement stepCycle: LAST / Resolution: 1.275→47.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 43 324 1904

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