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

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Basic information

Entry
Database: PDB / ID: 6hjh
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Mutual gliding-motility protein MglA
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 3, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mutual gliding-motility protein MglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4862
Polymers22,0421
Non-polymers4431
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-7 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.550, 73.550, 97.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Mutual gliding-motility protein MglA


Mass: 22042.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (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.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES 0.1M, PEG 4000 30%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.3→38.6 Å / Num. obs: 4841 / % possible obs: 47 % / Redundancy: 5.2 % / Biso Wilson estimate: 90.42 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.23 / Rrim(I) all: 0.26 / Net I/σ(I): 7.26
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.6 / Num. unique obs: 135 / CC1/2: 0.4 / Rrim(I) all: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T1O

3t1o


Resolution: 3.3→38.6 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.789 / Rfactor Rfree error: 0 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 1.104
RfactorNum. reflection% reflectionSelection details
Rfree0.316 112 4.95 %RANDOM
Rwork0.191 ---
obs0.197 2264 46.6 %-
Displacement parametersBiso mean: 103.94 Å2
Baniso -1Baniso -2Baniso -3
1-2.3935 Å20 Å20 Å2
2--2.3935 Å20 Å2
3----4.787 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: 1 / Resolution: 3.3→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 28 1 1548
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091577HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.092139HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d560SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes237HARMONIC5
X-RAY DIFFRACTIONt_it1577HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion23.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion207SEMIHARMONIC5
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_contact1768SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.256 -4.69 %
Rwork0.268 488 -
all0.267 512 -
obs--37.73 %
Refinement TLS params.Method: refined / Origin x: 40.1012 Å / Origin y: -10.3245 Å / Origin z: 1.8733 Å
111213212223313233
T0.1427 Å2-0.0164 Å2-0.1044 Å2--0.2096 Å2-0.004 Å2---0.117 Å2
L3.7278 °2-0.6349 °20.0845 °2-3.7529 °21.8815 °2--8.7741 °2
S0.0337 Å °0.2959 Å °-0.0177 Å °-0.168 Å °-0.0368 Å °-0.2244 Å °-0.1534 Å °0.1335 Å °0.0031 Å °
Refinement TLS groupSelection details: { A|3 - A|192 }

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