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- PDB-3t1s: MglB Homodimer -

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Basic information

Entry
Database: PDB / ID: 3t1s
TitleMglB Homodimer
ComponentsGliding protein MglB
KeywordsSIGNALING PROTEIN / GTPase activating protein / bacterial polarity / motility / Pole localisation / alpha/beta protein / catalytic GAP domain / Homodimer
Function / homology
Function and homology information


positive regulation of TOR signaling / guanyl-nucleotide exchange factor activity / molecular adaptor activity / identical protein binding / metal ion binding
Similarity search - Function
Ragulator complex protein LAMTOR2-like / Dynein light chain 2a, cytoplasmic / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable gliding protein (MglB)
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsMiertzschke, M. / Vetter, I.R. / Koerner, C. / Wittinghofer, A.
CitationJournal: Embo J. / Year: 2011
Title: Structural analysis of the Ras-like G protein MglA and its cognate GAP MglB and implications for bacterial polarity.
Authors: Miertzschke, M. / Koerner, C. / Vetter, I.R. / Keilberg, D. / Hot, E. / Leonardy, S. / Sogaard-Andersen, L. / Wittinghofer, A.
History
DepositionJul 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gliding protein MglB


Theoretical massNumber of molelcules
Total (without water)14,7011
Polymers14,7011
Non-polymers00
Water1,09961
1
A: Gliding protein MglB

A: Gliding protein MglB


Theoretical massNumber of molelcules
Total (without water)29,4022
Polymers29,4022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area2660 Å2
ΔGint-19 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.150, 36.150, 308.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Gliding protein MglB


Mass: 14700.823 Da / Num. of mol.: 1 / Fragment: MglB GAP amino acid 6-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1131 / Plasmid: pGexET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus RIL / References: UniProt: Q5SJ83
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.98 Å3/Da / Density % sol: 37.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.28M CaCl2, 7% Isopropanol, 30% Glycerol, 0.07 M Natrium-Acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.93 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.67→31.3 Å / Num. all: 15232 / Num. obs: 15213 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.67→1.71 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PRODCdata collection
MOLREPphasing
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J3W

1j3w


Resolution: 1.67→31.3 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.458 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27229 761 5 %RANDOM
Rwork0.21859 ---
all0.252 15232 --
obs0.2212 14452 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.373 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20.58 Å20 Å2
2--1.16 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 1.67→31.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 0 61 1076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221140
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1181.9971566
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76323.51954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68715206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2451511
X-RAY DIFFRACTIONr_chiral_restr0.150.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021880
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4531.5706
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.38221134
X-RAY DIFFRACTIONr_scbond_it3.7313434
X-RAY DIFFRACTIONr_scangle_it5.8724.5419
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 54 -
Rwork0.291 1035 -
obs--100 %

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