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- PDB-3t1t: MglA bound to GDP in P1 tetrameric arrangement -

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Basic information

Entry
Database: PDB / ID: 3t1t
TitleMglA bound to GDP in P1 tetrameric arrangement
ComponentsGliding protein mglA
KeywordsHYDROLASE / G domain containg protein / bacterial GTPase / Bacterial polarity / motility / alpha/beta protein
Function / homology
Function and homology information


GTPase activity / GTP binding / metal ion binding
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 / Probable gliding protein mglA
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_comp_id / _struct_conn.ptnr2_label_seq_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 mglA
C: Gliding protein mglA
D: Gliding protein mglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7088
Polymers88,9354
Non-polymers1,7734
Water2,522140
1
A: Gliding protein mglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6772
Polymers22,2341
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gliding protein mglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6772
Polymers22,2341
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Gliding protein mglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6772
Polymers22,2341
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Gliding protein mglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6772
Polymers22,2341
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.690, 62.860, 81.470
Angle α, β, γ (deg.)99.91, 100.14, 108.54
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Gliding protein mglA


Mass: 22233.781 Da / Num. of mol.: 4
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: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 65% MPD, 0.1M Tris-HCl , 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: 0.97874 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97874 Å / Relative weight: 1
ReflectionResolution: 1.9→44.73 Å / Num. obs: 66489 / % possible obs: 96.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.9→1.95 Å / Num. unique all: 4922 / % possible all: 96

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Processing

Software
NameVersionClassification
PRODCdata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.73 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.648 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A very preliminary model from low resolution SeMet data was used.
RfactorNum. reflection% reflectionSelection details
Rfree0.25378 3325 5 %RANDOM
Rwork0.20986 ---
all0.225 63777 --
obs0.21207 63162 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: 27.907 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0.23 Å20.6 Å2
2---0.84 Å20.57 Å2
3---1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5945 0 112 140 6197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0226333
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.9998630
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73823.191282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.147151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3041557
X-RAY DIFFRACTIONr_chiral_restr0.1390.2974
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214751
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_it1.3281.53812
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.27626200
X-RAY DIFFRACTIONr_scbond_it3.91732521
X-RAY DIFFRACTIONr_scangle_it5.8344.52415
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 246 -
Rwork0.253 4660 -
obs--100 %

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