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- PDB-3md0: Crystal structure of arginine/ornithine transport system ATPase f... -

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Basic information

Entry
Database: PDB / ID: 3md0
TitleCrystal structure of arginine/ornithine transport system ATPase from Mycobacterium tuberculosis bound to GDP (a RAS-like GTPase superfamily protein)
ComponentsArginine/ornithine transport system ATPase
KeywordsTRANSPORT PROTEIN / Seattle Structural Genomics Center for Infectious Disease / RAS / RAS-like GTPase / allosteric modulator / tuberculosis / ATP-binding / Nucleotide-binding / SSGCID
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
GUANOSINE-5'-DIPHOSPHATE / Probable GTPase Rv1496 / Probable GTPase Rv1496
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 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: 2014
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
DepositionMar 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 19, 2012Group: Database references
Revision 1.3Mar 11, 2015Group: Database references
Revision 1.4Jun 3, 2015Group: Database references
Revision 1.5Sep 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: Arginine/ornithine transport system ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0406
Polymers38,5971
Non-polymers4435
Water1,44180
1
A: Arginine/ornithine transport system ATPase
hetero molecules

A: Arginine/ornithine transport system ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,08012
Polymers77,1942
Non-polymers88610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6320 Å2
ΔGint-51 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.530, 187.360, 66.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Arginine/ornithine transport system ATPase


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: Rv1496 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: P63577, UniProt: P9WPZ1*PLUS
#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-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 50% PEG 200, 0.2 M NaCl, 0.1 M Na K phosphate pH 6.2, 22.0 mg/mL protein, 2 mM GDP, crystal tracking ID 207391d3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→19.96 Å / Num. obs: 15339 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.84 % / Biso Wilson estimate: 50.04 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.5
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 4.62 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.7 / Num. measured obs: 5035 / Num. unique obs: 1090 / % possible all: 97.2

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.85 Å19.96 Å
Translation2.85 Å19.96 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qm7

2qm7


Resolution: 2.45→19.96 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.821 / SU B: 15.932 / SU ML: 0.172 / SU R Cruickshank DPI: 0.354 / SU Rfree: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.354 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 780 5.1 %RANDOM
Rwork0.211 ---
obs0.213 15268 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 121.64 Å2 / Biso mean: 45.656 Å2 / Biso min: 15.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2---1.08 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.45→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 32 80 2326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212274
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9773112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3635297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61123.70889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82615346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1231519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211682
X-RAY DIFFRACTIONr_mcbond_it0.7941.51489
X-RAY DIFFRACTIONr_mcangle_it1.49722369
X-RAY DIFFRACTIONr_scbond_it2.3743785
X-RAY DIFFRACTIONr_scangle_it4.0254.5743
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 64 -
Rwork0.27 1018 -
all-1082 -
obs--96.87 %
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)
1-2.8444-3.7467-1.96298.1511-1.8189-2.7993-0.1167-0.6157-0.42330.0485-0.5891-0.81531.06-0.09970.70580.5080.1373-0.01480.07980.06390.842223.939411.68691.2487
20.6296-0.21520.53742.0419-0.53630.30590.2640.1702-0.1330.10870.0008-0.0880.18470.173-0.26480.20490.0369-0.0860.1609-0.07970.208919.275628.4559-0.4965
310.92495.676911.414211.548410.12739.87961.15561.7489-0.53070.23310.0356-2.43142.2251.7118-1.19120.23770.39970.19370.26210.00090.322726.779127.6837-4.618
40.3676-0.16830.46630.9616-0.19780.9791-0.02960.144-0.01420.0883-0.0044-0.06060.05790.00580.03410.1416-0.0133-0.00920.2023-0.00430.160110.154138.0271-6.2725
50.05530.38420.75122.77070.41953.0550.22530.029-0.1298-0.2267-0.0375-0.21810.3543-0.0043-0.18770.28860.0689-0.00640.1098-0.05170.17611.86789.4395-24.8454
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 41
2X-RAY DIFFRACTION2A42 - 94
3X-RAY DIFFRACTION3A111 - 134
4X-RAY DIFFRACTION4A135 - 277
5X-RAY DIFFRACTION5A278 - 333

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