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- PDB-6h35: Myxococcus xanthus MglA bound to GDP and Pi with mixed inactive a... -

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Basic information

Entry
Database: PDB / ID: 6h35
TitleMyxococcus xanthus MglA bound to GDP and Pi with mixed inactive and active switch region conformations
ComponentsMutual gliding-motility protein MglA
KeywordsCYTOSOLIC PROTEIN / small GTPase in a mixed state
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
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Mutual gliding-motility protein MglA
Similarity search - Component
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVarela, P.F. / Galicia, C. / Cherfils, J.
Funding support France, 1items
OrganizationGrant numberCountry
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 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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
B: Mutual gliding-motility protein MglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,78714
Polymers45,7432
Non-polymers2,04512
Water2,792155
1
A: Mutual gliding-motility protein MglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1189
Polymers22,8711
Non-polymers1,2478
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mutual gliding-motility protein MglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6695
Polymers22,8711
Non-polymers7984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.600, 116.650, 49.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-455-

HOH

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Components

#1: Protein Mutual gliding-motility protein MglA


Mass: 22871.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Small GTPase / Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Gene: mglA, MXAN_1925 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1DB04
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 70% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.299→50 Å / Num. obs: 93193 / % possible obs: 74.71 % / Redundancy: 5.3 % / Biso Wilson estimate: 38.07 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.076 / Net I/σ(I): 8.29
Reflection shellResolution: 2.299→2.38 Å / Mean I/σ(I) obs: 1.03 / Num. unique obs: 474 / CC1/2: 0.392 / % possible all: 20.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.11 Å / SU ML: 0.2609 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9156 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 848 4.85 %random
Rwork0.2135 16624 --
obs0.2155 17472 74.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 133 155 3364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343272
X-RAY DIFFRACTIONf_angle_d0.76374441
X-RAY DIFFRACTIONf_chiral_restr0.0475500
X-RAY DIFFRACTIONf_plane_restr0.0042544
X-RAY DIFFRACTIONf_dihedral_angle_d7.84892319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.3584490.3362804X-RAY DIFFRACTION22.25
2.44-2.630.3177690.29631392X-RAY DIFFRACTION38.26
2.63-2.90.29181570.28243157X-RAY DIFFRACTION86.06
2.9-3.320.27621850.22523676X-RAY DIFFRACTION99.87
3.32-4.180.23281960.18493719X-RAY DIFFRACTION99.92
4.18-49.120.24531920.1993876X-RAY DIFFRACTION99.51
Refinement TLS params.Method: refined / Origin x: 32.303813486 Å / Origin y: 14.7277344099 Å / Origin z: 70.125826273 Å
111213212223313233
T0.151727455952 Å20.0318632340516 Å20.000714965373303 Å2-0.157843902047 Å20.00456517040674 Å2--0.133104574667 Å2
L0.825014828201 °20.166458797225 °2-0.115500401313 °2-1.2346168088 °2-0.385856557353 °2--0.457698060692 °2
S-0.0460762224911 Å °0.0402299587653 Å °-0.0186976574689 Å °0.0617549787103 Å °0.10560452117 Å °0.143531617216 Å °0.0145643759255 Å °0.018149100068 Å °0.00895288325152 Å °
Refinement TLS groupSelection details: all

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