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- PDB-3nxs: Crystal structure of LAO/AO transport system from Mycobacterium s... -

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Basic information

Entry
Database: PDB / ID: 3nxs
TitleCrystal structure of LAO/AO transport system from Mycobacterium smegmatis bound to GDP
ComponentsLAO/AO transport system ATPase
KeywordsTRANSPORT PROTEIN / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Mycobacterium / pathogenic bacterium / tuberculosis / methylmalonic aciduria / ortholog / RAS-like GTPase superfamily / G-domain / arginine / ornithine / transport system / GTPAse / mislabeled as an ATPase / metallochaperone
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups / transferase 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle ...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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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
GUANOSINE-5'-DIPHOSPHATE / LAO/AO transport system ATPase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 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: LAO/AO transport system ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0043
Polymers35,5261
Non-polymers4792
Water1,62190
1
A: LAO/AO transport system ATPase
hetero molecules

A: LAO/AO transport system ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0086
Polymers71,0512
Non-polymers9574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4910 Å2
ΔGint-47 kcal/mol
Surface area26690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.630, 91.460, 57.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein LAO/AO transport system ATPase


Mass: 35525.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_3160 / Production host: Escherichia coli (E. coli)
References: UniProt: A0QX37, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9
Details: JCSG+ condition F6, 0.1% Bicine pH 9.0, 10% MPD as crystallant, 28.66 mg/mL protein, crystal tracking ID 215415f6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 19008 / Num. obs: 18658 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 52.616 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 22.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.360.4894.312010132597.9
2.36-2.420.3885.411939131898
2.42-2.490.3186.711621128998
2.49-2.570.256811316125798.3
2.57-2.660.2169.210765119398.1
2.66-2.750.171210522117997.9
2.75-2.850.14514.110257114298
2.85-2.970.117179769109898.4
2.97-3.10.08921.49216105998.7
3.1-3.250.07268822101898.2
3.25-3.430.05532.2826796798.5
3.43-3.640.0536.4768491698.8
3.64-3.890.04340.8715186598.5
3.89-4.20.0443.1658881098.4
4.2-4.60.03945.8606275598.6
4.6-5.140.03646.9542768999
5.14-5.940.03645.3507260899.5
5.94-7.270.03347.3438153599.3
7.27-10.290.02550.3335541899.1
10.290.02149.3161821783.5

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Phasing

Phasing MRRfactor: 51.28 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.87 Å
Translation3 Å19.87 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: 3MD0

3md0


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2291 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.843 / SU B: 12.7 / SU ML: 0.14 / SU R Cruickshank DPI: 0.2704 / SU Rfree: 0.2017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 943 5.1 %RANDOM
Rwork0.2086 ---
obs0.2098 18582 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.59 Å2 / Biso mean: 56.8727 Å2 / Biso min: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.13 Å20 Å20 Å2
2--1.18 Å20 Å2
3---1.95 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 29 90 2402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212354
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9783212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9565306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04522.95998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16715377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5321525
X-RAY DIFFRACTIONr_chiral_restr0.10.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211760
X-RAY DIFFRACTIONr_mcbond_it0.9311.51519
X-RAY DIFFRACTIONr_mcangle_it1.75722425
X-RAY DIFFRACTIONr_scbond_it2.6583835
X-RAY DIFFRACTIONr_scangle_it4.4184.5786
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 69 -
Rwork0.245 1247 -
all-1316 -
obs--96.98 %
Refinement TLS params.Method: refined / Origin x: 27.8404 Å / Origin y: 10.5032 Å / Origin z: 1.4216 Å
111213212223313233
T0.0533 Å20.0289 Å2-0.0361 Å2-0.1031 Å2-0.0871 Å2--0.1238 Å2
L0.5643 °2-0.1544 °2-0.1166 °2-0.4572 °2-0.0082 °2--0.0889 °2
S0.0171 Å °-0.0874 Å °0.1135 Å °-0.0639 Å °-0.0365 Å °0.1024 Å °-0.0343 Å °-0.0153 Å °0.0193 Å °

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