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- PDB-4rmf: Biochemical and structural characterization of mycobacterial aspa... -

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Basic information

Entry
Database: PDB / ID: 4rmf
TitleBiochemical and structural characterization of mycobacterial aspartyl-tRNA synthetase AspS, a promising TB drug target
ComponentsAspartate--tRNA(Asp/Asn) ligase
KeywordsLIGASE / alpha and beta proteins / tRNA synthetase / tRNA
Function / homology
Function and homology information


aspartate-tRNAAsn ligase / aspartate-tRNA(Asn) ligase activity / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
GAD-like domain / : / : / Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) ...GAD-like domain / : / : / Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Gyrase A; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2,2-bis(hydroxymethyl)propane-1,3-diol / FORMIC ACID / Aspartate--tRNA(Asp/Asn) ligase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCox, J.A.G. / Gurcha, S.S. / Veeraraghavan, U. / Besra, G.S. / Futterer, K.
CitationJournal: Plos One / Year: 2014
Title: Biochemical and Structural Characterization of Mycobacterial Aspartyl-tRNA Synthetase AspS, a Promising TB Drug Target.
Authors: Gurcha, S.S. / Usha, V. / Cox, J.A. / Futterer, K. / Abrahams, K.A. / Bhatt, A. / Alderwick, L.J. / Reynolds, R.C. / Loman, N.J. / Nataraj, V. / Alemparte, C. / Barros, D. / Lloyd, A.J. / ...Authors: Gurcha, S.S. / Usha, V. / Cox, J.A. / Futterer, K. / Abrahams, K.A. / Bhatt, A. / Alderwick, L.J. / Reynolds, R.C. / Loman, N.J. / Nataraj, V. / Alemparte, C. / Barros, D. / Lloyd, A.J. / Ballell, L. / Hobrath, J.V. / Besra, G.S.
History
DepositionOct 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Sep 20, 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: Aspartate--tRNA(Asp/Asn) ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7123
Polymers66,5301
Non-polymers1822
Water2,234124
1
A: Aspartate--tRNA(Asp/Asn) ligase
hetero molecules

A: Aspartate--tRNA(Asp/Asn) ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,4246
Polymers133,0592
Non-polymers3644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9180 Å2
ΔGint-36 kcal/mol
Surface area46790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.609, 141.514, 156.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-810-

HOH

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Components

#1: Protein Aspartate--tRNA(Asp/Asn) ligase / Aspartyl-tRNA synthetase / AspRS / Non-discriminating aspartyl-tRNA synthetase / ND-AspRS


Mass: 66529.742 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: aspS, MSMEG_3003, MSMEI_2928 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QWN3, aspartate-tRNAAsn ligase
#2: Chemical ChemComp-3SY / 2,2-bis(hydroxymethyl)propane-1,3-diol / Pentaerythritol


Mass: 136.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O4
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30 % (v/v) pentaerythritol ethoxylate, 0.1 M magnesium formate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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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: May 16, 2014 / Details: VariMax
RadiationMonochromator: multi-layer mirrors (VariMax) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→42.04 Å / Num. all: 31382 / Num. obs: 31382 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.5 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 25.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C0A

1c0a


Resolution: 2.4→42.04 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.905 / SU B: 13.909 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24462 1580 5 %RANDOM
Rwork0.21519 ---
all0.2152 29771 --
obs0.21671 29771 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.172 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å2-0 Å2
2--0.4 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4323 0 12 124 4459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194436
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9566040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.295578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.61723.01196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82115635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2751538
X-RAY DIFFRACTIONr_chiral_restr0.0830.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213484
LS refinement shellResolution: 2.403→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 105 -
Rwork0.263 1971 -
obs--96.38 %
Refinement TLS params.Method: refined / Origin x: -34.759 Å / Origin y: -15.784 Å / Origin z: 8.797 Å
111213212223313233
T0.1094 Å2-0.047 Å2-0.0073 Å2-0.1532 Å20.0194 Å2--0.0478 Å2
L0.431 °20.2336 °2-0.0139 °2-0.9762 °20.1056 °2--0.5205 °2
S0.0673 Å °-0.1022 Å °-0.1063 Å °0.0807 Å °-0.115 Å °0.0613 Å °0.103 Å °-0.1717 Å °0.0477 Å °

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