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- PDB-6h5b: Myxococcus xanthus MglA in complex with its GAP MglB and GTPgammaS -

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Basic information

Entry
Database: PDB / ID: 6h5b
TitleMyxococcus xanthus MglA in complex with its GAP MglB and GTPgammaS
Components
  • MglB
  • Mutual gliding-motility protein MglA
KeywordsCYTOSOLIC PROTEIN / GTPase and GAP complex
Function / homology
Function and homology information


positive regulation of TOR signaling / guanyl-nucleotide exchange factor activity / regulation of protein localization / molecular adaptor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Ragulator complex protein LAMTOR2-like / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / 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 / DI(HYDROXYETHYL)ETHER / Mutual gliding-motility protein MglA / Dynein regulation protein LC7
Similarity search - Component
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
Myxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 24, 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: Refinement description / Structure summary / Category: software / struct / Item: _software.name / _struct.title

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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: MglB
C: MglB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,23912
Polymers57,4043
Non-polymers1,8359
Water23413
1
A: Mutual gliding-motility protein MglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1506
Polymers22,8711
Non-polymers1,2785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MglB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4793
Polymers17,2671
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MglB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6113
Polymers17,2671
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.101, 135.101, 60.382
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
121(chain 'B' and (resid 12 through 20 or (resid 21...B12 - 37
131(chain 'B' and (resid 12 through 20 or (resid 21...B40 - 44
141(chain 'B' and (resid 12 through 20 or (resid 21...B47 - 69
151(chain 'B' and (resid 12 through 20 or (resid 21...B72 - 75
161(chain 'B' and (resid 12 through 20 or (resid 21...B77 - 97
171(chain 'B' and (resid 12 through 20 or (resid 21...B99 - 106
181(chain 'B' and (resid 12 through 20 or (resid 21...B109 - 129
291(chain 'C' and (resid 12 through 20 or (resid 21...C12 - 37
2101(chain 'C' and (resid 12 through 20 or (resid 21...C40 - 44
2111(chain 'C' and (resid 12 through 20 or (resid 21...C47 - 69
2121(chain 'C' and (resid 12 through 20 or (resid 21...C72 - 75
2131(chain 'C' and (resid 12 through 20 or (resid 21...C77 - 97
2141(chain 'C' and (resid 12 through 20 or (resid 21...C99 - 106
2151(chain 'C' and (resid 12 through 20 or (resid 21...C109 - 129

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein Mutual gliding-motility protein MglA


Mass: 22871.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GTPgS / Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Gene: mglA, MXAN_1925 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1DB04
#2: Protein MglB


Mass: 17266.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PEG from condition / Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: mglB / Production host: Escherichia coli (E. coli) / References: UniProt: Q50883

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Non-polymers , 6 types, 22 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 55.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M HEPES, 16% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.979336 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979336 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 10926 / % possible obs: 69.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 76.87 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.03 / Rrim(I) all: 0.07551 / Net I/σ(I): 14.49
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1810 / CC1/2: 0.658 / Rpim(I) all: 0.44

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45.02 Å / SU ML: 0.3885 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.7263
RfactorNum. reflection% reflection
Rfree0.2554 1102 10.09 %
Rwork0.1987 --
obs0.2044 10924 69.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 69.24 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 116 13 3552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393581
X-RAY DIFFRACTIONf_angle_d0.73044818
X-RAY DIFFRACTIONf_chiral_restr0.0456561
X-RAY DIFFRACTIONf_plane_restr0.0042598
X-RAY DIFFRACTIONf_dihedral_angle_d17.70882171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.4531390.3555350X-RAY DIFFRACTION20.05
2.93-3.080.3556530.3252480X-RAY DIFFRACTION27.29
3.08-3.270.4095830.2935725X-RAY DIFFRACTION42.15
3.27-3.530.32041360.24531190X-RAY DIFFRACTION68.17
3.53-3.880.27261910.21511736X-RAY DIFFRACTION99.02
3.88-4.440.25091980.18041767X-RAY DIFFRACTION99.8
4.44-5.60.23711910.17451780X-RAY DIFFRACTION99.9
5.6-45.020.22492110.18871794X-RAY DIFFRACTION98.38
Refinement TLS params.Method: refined / Origin x: -52.3295124017 Å / Origin y: -17.815975229 Å / Origin z: 7.06471596382 Å
111213212223313233
T0.218691338988 Å20.0506684417462 Å2-0.0215110603979 Å2--0.420535707191 Å20.364296858535 Å2--0.245109456691 Å2
L1.51030802783 °2-0.401513899737 °2-0.59784594951 °2-1.83334237004 °20.881604522361 °2--2.58712516432 °2
S0.173450543134 Å °0.421229606189 Å °-0.217281262809 Å °0.0147199909988 Å °0.286822269332 Å °-0.849465387347 Å °-0.571465965381 Å °1.05058764201 Å °2.81700830684 Å °
Refinement TLS groupSelection details: all

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