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- PDB-3tk1: Crystal structure of a MeaB and Rv1496 ortholog from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 3tk1
TitleCrystal structure of a MeaB and Rv1496 ortholog from Mycobacterium thermoresistible bound to GDP
ComponentsMembrane ATPase/protein kinase
KeywordsHYDROLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / MeaB / MMAA / methylmalonic aciduria / Rv1496 / thermophile / GDP / RAS-like GTPase / G-protein
Function / homology
Function and homology information


kinase activity / GTPase activity / GTP binding
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 / Membrane ATPase/protein kinase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: 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.
#1: Journal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionAug 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references / Source and taxonomy
Revision 1.3Apr 22, 2015Group: Database references
Revision 1.4Jun 3, 2015Group: Database references
Revision 1.5Sep 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: Membrane ATPase/protein kinase
B: Membrane ATPase/protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2625
Polymers71,3402
Non-polymers9223
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-68 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.380, 106.430, 134.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Membrane ATPase/protein kinase


Mass: 35669.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria)
Strain: ATCC 19527 / Gene: KEK_00260 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli)
References: UniProt: G7CAR0, Hydrolases; Acting on acid anhydrides
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.12 Å3/Da / Density % sol: 41.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MythA.00200.a.A1 PS00590 at 42.4 mg/mL with 2 mM GDP against PACT screen condition B10, 0.2 M MgCl2, 0.1 M MES pH 6.0, 20% PEG 6000 with 25% ethylene glycol as cryo-protectant, crystal ...Details: MythA.00200.a.A1 PS00590 at 42.4 mg/mL with 2 mM GDP against PACT screen condition B10, 0.2 M MgCl2, 0.1 M MES pH 6.0, 20% PEG 6000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 215739b10, 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: Jul 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 24555 / Num. obs: 23270 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 44.319 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.460.5193.029128174397.8
2.46-2.530.4783.488635168996.6
2.53-2.60.3644.278805164697.1
2.6-2.680.3255.058177158396.4
2.68-2.770.2885.48246152696.8
2.77-2.870.236.788014149996.3
2.87-2.980.1758.727768143196.3
2.98-3.10.14510.87596139696.2
3.1-3.240.11613.217075133395.6
3.24-3.390.0916.846564125095.3
3.39-3.580.07621.56137119894
3.58-3.790.06126.15416109391
3.79-4.060.05330.455067102191.2
4.06-4.380.03636.95339100193.9
4.38-4.80.03340.33489392493.7
4.8-5.370.03438.84443084093.2
5.37-6.20.04333.12379772891.9
6.2-7.590.02941.46334863191.3
7.59-10.730.0257.93266650090.7
10.730.01862.89119223872.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.54 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.3 Å19.84 Å
Translation3.3 Å19.84 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MD0

3md0


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.2415 / WRfactor Rwork: 0.1939 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8111 / SU B: 18.044 / SU ML: 0.211 / SU R Cruickshank DPI: 0.7755 / SU Rfree: 0.3297 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.775 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 2369 10.2 %RANDOM
Rwork0.2243 ---
obs0.2296 23269 94.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.96 Å2 / Biso mean: 37.3745 Å2 / Biso min: 8.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2---1.06 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4435 0 57 107 4599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194554
X-RAY DIFFRACTIONr_bond_other_d0.0040.022908
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9826210
X-RAY DIFFRACTIONr_angle_other_deg1.17637101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10323.03165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51315717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.921542
X-RAY DIFFRACTIONr_chiral_restr0.0710.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025098
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02888
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 175 -
Rwork0.289 1422 -
all-1597 -
obs--97.56 %
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)
10.4627-0.3573-0.63260.7730.13621.11780.0848-0.18180.0099-0.0942-0.06030.0225-0.10980.4035-0.02450.0533-0.0732-0.0380.22060.03870.05-16.55446.6226-21.2493
20.27690.1232-0.05680.4449-0.03420.1541-0.03720.04570.00870.09450.0952-0.0574-0.0082-0.0331-0.05790.07950.0151-0.02420.046-0.01510.088-35.5887-1.95540.9304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 325
2X-RAY DIFFRACTION2B4 - 326

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