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- PDB-5ymx: Myxococcus xanthus MglA in GDP bound conformation -

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Basic information

Entry
Database: PDB / ID: 5ymx
TitleMyxococcus xanthus MglA in GDP bound conformation
ComponentsMutual gliding-motility protein MglA
KeywordsSIGNALING PROTEIN / HYDROLASE / Small Ras-like GTPase / Cytosolic / Myxococcus motility protein / spatial oscillation
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 / IMIDAZOLE / Mutual gliding-motility protein MglA
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBaranwal, J. / Gayathri, P.
Funding support India, 1items
OrganizationGrant numberCountry
INSPIREIFA12-LSBM52 India
CitationJournal: Plos Biol. / Year: 2019
Title: Allosteric regulation of a prokaryotic small Ras-like GTPase contributes to cell polarity oscillations in bacterial motility.
Authors: Baranwal, J. / Lhospice, S. / Kanade, M. / Chakraborty, S. / Gade, P.R. / Harne, S. / Herrou, J. / Mignot, T. / Gayathri, P.
History
DepositionOct 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: 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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Mutual gliding-motility protein MglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2989
Polymers46,0312
Non-polymers1,2677
Water7,638424
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A: Mutual gliding-motility protein MglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7085
Polymers23,0151
Non-polymers6934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-12 kcal/mol
Surface area10960 Å2
MethodPISA
2
B: Mutual gliding-motility protein MglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5904
Polymers23,0151
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.340, 68.610, 89.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Mutual gliding-motility protein MglA


Mass: 23015.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria)
Strain: DK 1622 / Gene: mglA, MXAN_1925 / Plasmid: pHis17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q1DB04, small monomeric GTPase

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Non-polymers , 5 types, 431 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30% 2-Methyl 2,4-pentane diol (MPD), 10% PEG 4000, 100mM Imidazole, pH 8.0
PH range: 6.5 - 8.0 / Temp details: plates kept in an incubator at 291 K

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nil
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2014 / Details: Bent collimating mirror and torroid
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.35→32.03 Å / Num. obs: 91269 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 15.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.022 / Rrim(I) all: 0.06 / Rsym value: 0.06 / Net I/av σ(I): 8 / Net I/σ(I): 14.6
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 13188 / CC1/2: 0.784 / Rpim(I) all: 0.294 / Rrim(I) all: 0.791 / Rsym value: 0.791 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T12

3t12


Resolution: 1.35→28.924 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1787 4587 5.04 %
Rwork0.1505 --
obs0.152 91051 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→28.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 82 424 3651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053388
X-RAY DIFFRACTIONf_angle_d0.8784614
X-RAY DIFFRACTIONf_dihedral_angle_d15.3831267
X-RAY DIFFRACTIONf_chiral_restr0.076519
X-RAY DIFFRACTIONf_plane_restr0.004581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.3121450.25612848X-RAY DIFFRACTION100
1.3653-1.38140.32011620.25722837X-RAY DIFFRACTION100
1.3814-1.39830.24671430.20292906X-RAY DIFFRACTION100
1.3983-1.4160.22161440.18282840X-RAY DIFFRACTION100
1.416-1.43460.22511570.17692847X-RAY DIFFRACTION100
1.4346-1.45420.22321570.17912859X-RAY DIFFRACTION100
1.4542-1.4750.19751400.17962872X-RAY DIFFRACTION100
1.475-1.4970.19051610.15672847X-RAY DIFFRACTION100
1.497-1.52040.1811590.16682837X-RAY DIFFRACTION100
1.5204-1.54530.1951730.14962854X-RAY DIFFRACTION100
1.5453-1.5720.16311270.12582885X-RAY DIFFRACTION100
1.572-1.60060.14241520.12072892X-RAY DIFFRACTION100
1.6006-1.63140.19341400.13112852X-RAY DIFFRACTION100
1.6314-1.66460.17161540.12972864X-RAY DIFFRACTION100
1.6646-1.70080.16991440.13662884X-RAY DIFFRACTION100
1.7008-1.74040.19041530.1292884X-RAY DIFFRACTION100
1.7404-1.78390.1681600.12692868X-RAY DIFFRACTION100
1.7839-1.83210.18121530.12892875X-RAY DIFFRACTION100
1.8321-1.8860.17391640.13462893X-RAY DIFFRACTION100
1.886-1.94690.20421370.14912889X-RAY DIFFRACTION100
1.9469-2.01650.1691600.13772893X-RAY DIFFRACTION100
2.0165-2.09720.18771590.14622876X-RAY DIFFRACTION100
2.0972-2.19260.17431610.14242907X-RAY DIFFRACTION100
2.1926-2.30820.17141430.14592901X-RAY DIFFRACTION100
2.3082-2.45270.16091570.14712911X-RAY DIFFRACTION100
2.4527-2.6420.19251500.15542928X-RAY DIFFRACTION100
2.642-2.90760.18551580.15832938X-RAY DIFFRACTION100
2.9076-3.32780.16361550.15082948X-RAY DIFFRACTION100
3.3278-4.19070.14781680.13352963X-RAY DIFFRACTION99
4.1907-28.93050.19231510.17222866X-RAY DIFFRACTION92

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