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- PDB-6hjo: Myxococcus xanthus MglA bound to GDP -

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Basic information

Entry
Database: PDB / ID: 6hjo
TitleMyxococcus xanthus MglA bound to GDP
ComponentsMutual gliding-motility protein MglA
KeywordsCYTOSOLIC PROTEIN / Small GTPase
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 / Mutual gliding-motility protein MglA
Similarity search - Component
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsVarela, P.F. / Cherfils, J.
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
DepositionSep 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / refine_ls_shell
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low

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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)44,9714
Polymers44,0852
Non-polymers8862
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer in certain conditions
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-15 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.980, 89.180, 118.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mutual gliding-motility protein MglA


Mass: 22042.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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 / Guanosine 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.24 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate pH 6.5, 40% MPD and PEG 8 000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.98→36.13 Å / Num. obs: 40545 / % possible obs: 98 % / Redundancy: 4.4 % / Biso Wilson estimate: 33.56 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1209 / Rrim(I) all: 0.1364 / Net I/σ(I): 13.07
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3634 / CC1/2: 0.744 / Rrim(I) all: 1.276 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T1O

3t1o


Resolution: 1.98→36.13 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.182 / SU Rfree Blow DPI: 0.152 / SU Rfree Cruickshank DPI: 0.155
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1740 5.17 %RANDOM
Rwork0.227 ---
obs0.227 33686 53 %-
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.3564 Å20 Å20 Å2
2---7.0122 Å20 Å2
3----1.3442 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 1.98→36.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 56 74 3180
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013166HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.034294HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1124SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes554HARMONIC5
X-RAY DIFFRACTIONt_it3166HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion17.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion416SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3634SEMIHARMONIC4
LS refinement shellResolution: 1.98→2.05 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.1944 -5.04 %
Rwork0.2098 640 -
all0.209 674 -
obs--5.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.539-0.34830.00084.0733-0.38171.56070.0215-0.01230.17170.693-0.1489-0.1014-0.06850.0740.12750.1265-0.0625-0.0565-0.1630.0119-0.0873-29.5665-23.030324.3209
22.42890.1421-0.24331.92360.54584.55580.2308-0.25790.1267-0.12360.03090.0326-0.6457-0.2594-0.26170.09040.09990.0512-0.11760.0399-0.0671-21.49172.6294-1.2897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|2 - A|200 }
2X-RAY DIFFRACTION2{ B|2 - B|200 }

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