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- PDB-4gt1: Crystal structure of a MeaB- and MMAA-like GTPase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 4gt1
TitleCrystal structure of a MeaB- and MMAA-like GTPase from Mycobacterium tuberculosis bound to 2'-deoxyguanosine diphosphate
ComponentsProbable GTPase Rv1496/MT1543
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Mycobacterium / GTPase / ATPase / substrate-specificity / G-protein / Ras-like GTPase / ArgK superfamily / chain swapped homodimer
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-DIPHOSPHATE / TRIETHYLENE GLYCOL / Probable GTPase Rv1496 / Probable GTPase Rv1496
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
DepositionAug 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Jun 3, 2015Group: Database references
Revision 1.4Sep 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 / 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)39,3605
Polymers38,5971
Non-polymers7634
Water2,522140
1
A: Probable GTPase Rv1496/MT1543
hetero molecules

A: Probable GTPase Rv1496/MT1543
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,72010
Polymers77,1942
Non-polymers1,5268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7280 Å2
ΔGint-56 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.920, 187.820, 66.460
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) / Strain: H37Rv / Gene: MT1543, MTCY277.18, Rv1496 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli)
References: UniProt: P63577, UniProt: P9WPZ1*PLUS, Hydrolases; Acting on acid anhydrides
#2: Chemical ChemComp-DGI / 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE


Type: DNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: MytuD.00200.a.A1 at 22 mg/mL with 4 mM dGTP against 0.1 M NaKHPO4, 48% PEG 200, 0.2 M NaCl, crystal tracking ID 236287b6, unique puck ID aqu7-6, pH 5.9, 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: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 28351 / Num. obs: 28337 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 36.499 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 29.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.050.4654.66167592041100
2.05-2.110.3616.05165032017100
2.11-2.170.2957.46160131961100
2.17-2.240.2389.24156441907100
2.24-2.310.19910.9615148184799.9
2.31-2.390.15913.28147421805100
2.39-2.480.14314.7139821712100
2.48-2.580.11318.38136201665100
2.58-2.70.09421.83131071607100
2.7-2.830.07227.25125451537100
2.83-2.980.06131.7211973147299.9
2.98-3.160.04839.09112141390100
3.16-3.380.03750.04103311291100
3.38-3.650.0359.9597801228100
3.65-40.02667.0688701139100
4-4.470.0227579281039100
4.47-5.160.01978.917096909100
5.16-6.320.02272.056212784100
6.32-8.940.01683.01480762099.7
8.940.01389.32254736697.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3md0

3md0


Resolution: 2→45.45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.273 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1431 5.1 %RANDOM
Rwork0.1889 ---
obs0.1908 28336 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.51 Å2 / Biso mean: 38.2709 Å2 / Biso min: 15.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å20 Å20 Å2
2---1.37 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 48 140 2386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192279
X-RAY DIFFRACTIONr_bond_other_d0.0010.022219
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9853111
X-RAY DIFFRACTIONr_angle_other_deg0.83235042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9945301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77123.44887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7515341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3921520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02487
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 128 -
Rwork0.221 1910 -
all-2038 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 12.3135 Å / Origin y: 28.1008 Å / Origin z: -8.1957 Å
111213212223313233
T0.0341 Å20.0271 Å2-0.0212 Å2-0.092 Å2-0.018 Å2--0.0608 Å2
L0.3515 °20.2641 °20.4984 °2-0.6269 °20.2658 °2--0.7407 °2
S0.1077 Å °0.0847 Å °-0.0676 Å °0.083 Å °-0.0036 Å °-0.0849 Å °0.155 Å °0.1298 Å °-0.1041 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 333
2X-RAY DIFFRACTION1A335 - 404

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