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- PDB-3p32: Hydrolysis of GTP to GDP by an MCM-associated and MeaB- and MMAA-... -

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Basic information

Entry
Database: PDB / ID: 3p32
TitleHydrolysis of GTP to GDP by an MCM-associated and MeaB- and MMAA-like G-protein from Mycobacterium tuberculosis
ComponentsProbable GTPase Rv1496/MT1543
KeywordsHYDROLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / MeaB / MMAA / methylmalonic aciduria protein a / GTPase / G-protein / MCM / methylmalonyl-CoA mutase / incorrectly assigned as an arginine/ornithine transport system ATPase / methylmaolonyl pathway
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides / GTPase activity / GTP binding / ATP binding / cytoplasm
Similarity search - Function
SIMIBI class G3E GTPase, ArgK/MeaB / Methylmalonyl Co-A mutase-associated GTPase MeaB / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...SIMIBI class G3E GTPase, ArgK/MeaB / Methylmalonyl Co-A mutase-associated GTPase MeaB / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / TRIETHYLENE GLYCOL / Probable GTPase Rv1496 / Probable GTPase Rv1496
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: J.Struct.Funct.Genom. / Year: 2015
Title: Crystal structures of Mycobacterial MeaB and MMAA-like GTPases.
Authors: Edwards, T.E. / Baugh, L. / Bullen, J. / Baydo, R.O. / Witte, P. / Thompkins, K. / Phan, I.Q. / Abendroth, J. / Clifton, M.C. / Sankaran, B. / Van Voorhis, W.C. / Myler, P.J. / Staker, B.L. ...Authors: Edwards, T.E. / Baugh, L. / Bullen, J. / Baydo, R.O. / Witte, P. / Thompkins, K. / Phan, I.Q. / Abendroth, J. / Clifton, M.C. / Sankaran, B. / Van Voorhis, W.C. / Myler, P.J. / Staker, B.L. / Grundner, C. / Lorimer, D.D.
History
DepositionOct 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Jun 3, 2015Group: Database references
Revision 1.4Sep 6, 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 / 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_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: Probable GTPase Rv1496/MT1543
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3404
Polymers38,5971
Non-polymers7443
Water2,522140
1
A: Probable GTPase Rv1496/MT1543
hetero molecules

A: Probable GTPase Rv1496/MT1543
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6818
Polymers77,1942
Non-polymers1,4876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7210 Å2
ΔGint-39 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.860, 188.220, 66.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Probable GTPase Rv1496/MT1543


Mass: 38596.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1543, MTCY277.18, Rv1496 / Production host: Escherichia coli (E. coli)
References: UniProt: P63577, UniProt: P9WPZ1*PLUS, Hydrolases; Acting on acid anhydrides
#2: 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
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 22.0 mg/mL MytuD00200aA1 PW25862 against 48% PEG 200, 0.1 M Na/K phosphate pH 6.2, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 33060 / Num. obs: 32985 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 36.61 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 25.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.950.5553.517610240999.4
1.95-20.3745174732347100
2-2.060.2736.616969227699.9
2.06-2.120.2128.816202221899.9
2.12-2.190.15711.1160942146100
2.19-2.270.1451315061209799.5
2.27-2.360.1111614807199899.8
2.36-2.450.09218.3146931969100
2.45-2.560.07422.113806185399.9
2.56-2.690.06325.613195178499.9
2.69-2.830.05230.6125651702100
2.83-30.04634.7118041620100
3-3.210.03941.4109891522100
3.21-3.470.0344810188142899.7
3.47-3.80.032549232130799.9
3.8-4.250.02856.58284120199.7
4.25-4.910.02461.77610106499.9
4.91-6.010.02360.4656691199.9
6.01-8.50.02261.8516272699.9
8.50.01763.3263740794.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MDO

3mdo


Resolution: 1.9→45.427 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2196 / WRfactor Rwork: 0.1973 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8536 / SU B: 5.836 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1303 / SU Rfree: 0.1209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 1670 5.1 %RANDOM
Rwork0.1986 ---
obs0.1998 32897 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.08 Å2 / Biso mean: 40.8061 Å2 / Biso min: 17.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2---1.23 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 48 140 2443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212348
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9863202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.685305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27523.47892
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13115354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5261521
X-RAY DIFFRACTIONr_chiral_restr0.0970.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211728
X-RAY DIFFRACTIONr_mcbond_it0.9231.51517
X-RAY DIFFRACTIONr_mcangle_it1.65322418
X-RAY DIFFRACTIONr_scbond_it2.4233831
X-RAY DIFFRACTIONr_scangle_it4.0454.5783
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 112 -
Rwork0.324 2285 -
all-2397 -
obs--98.97 %
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)
11.00550.08830.42481.2442-0.37160.16620.22170.2123-0.26370.02420.011-0.18160.14850.1596-0.23270.27320.082-0.11170.1763-0.08840.289120.546323.8091-1.7719
20.1564-0.14990.32230.1936-0.02421.0748-0.04310.09930.02810.047-0.00970.0078-0.02790.07280.05280.1757-0.0152-0.00880.26040.01410.20199.761344.124-9.6764
30.194-0.01450.51512.64761.76251.6802-0.0129-0.1148-0.08150.09250.07150.11890.1052-0.0202-0.05870.2596-0.03790.00460.15510.01560.23243.848624.5299-1.4382
40.1109-2.49441.20266.8560.68283.51120.4105-0.0878-0.135-0.74980.01610.1040.14770.2134-0.42660.43610.0822-0.04870.0171-0.04670.12421.23357.6293-31.4455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 165
2X-RAY DIFFRACTION2A166 - 257
3X-RAY DIFFRACTION3A258 - 292
4X-RAY DIFFRACTION4A293 - 333

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