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- PDB-3t12: MglA in complex with MglB in transition state -

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Basic information

Entry
Database: PDB / ID: 3t12
TitleMglA in complex with MglB in transition state
Components(Gliding protein ...) x 2
KeywordsHYDROLASE/SIGNALING PROTEIN / G-domain containing protein / Bacterial Polarity / Motility / Homodimeric GAP protein / Pole localisation / alpha/beta proteins / GTPase / HYDROLASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


positive regulation of TOR signaling / guanyl-nucleotide exchange factor activity / molecular adaptor activity / GTPase activity / GTP binding / metal ion binding / identical protein binding
Similarity search - Function
: / Ragulator complex protein LAMTOR2-like / Dynein light chain 2a, cytoplasmic / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases ...: / Ragulator complex protein LAMTOR2-like / Dynein light chain 2a, cytoplasmic / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Probable gliding protein mglA / Probable gliding protein (MglB)
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 21, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gliding protein mglA
B: Gliding protein MglB
C: Gliding protein MglB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2718
Polymers50,6523
Non-polymers6195
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-36 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.500, 174.200, 69.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-153-

HOH

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Components

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Gliding protein ... , 2 types, 3 molecules ABC

#1: Protein Gliding protein mglA


Mass: 21999.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1132 / Plasmid: pGexET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus RIL / References: UniProt: Q5SJ82, small monomeric GTPase
#2: Protein Gliding protein MglB


Mass: 14326.399 Da / Num. of mol.: 2 / Fragment: UNP residues 6-139 / Mutation: E14A, R15A, G65S, R124A, E127A, R131A
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

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Non-polymers , 4 types, 197 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 3.17 Å3/Da / Density % sol: 61.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris, 15% PEG 8000 , pH 8.5, 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: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.2→45.43 Å / Num. all: 33110 / Num. obs: 32905 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.3 Å / % possible all: 98.5

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Processing

Software
NameVersionClassification
PRODCdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J3W

1j3w


Resolution: 2.2→45.43 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.289 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24935 1646 5 %RANDOM
Rwork0.19518 ---
obs0.19791 31259 100 %-
all-33110 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.207 Å2
Baniso -1Baniso -2Baniso -3
1-4.81 Å20 Å20 Å2
2---3.27 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 36 192 3602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223532
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.9994814
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45623.784148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92815593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0171525
X-RAY DIFFRACTIONr_chiral_restr0.1550.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212637
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_it1.3261.52217
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34823544
X-RAY DIFFRACTIONr_scbond_it3.82131315
X-RAY DIFFRACTIONr_scangle_it6.1074.51262
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 118 -
Rwork0.24 2239 -
obs--100 %

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