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- PDB-4o2d: Crystal structure of aspartyl-tRNA synthetase from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 4o2d
TitleCrystal structure of aspartyl-tRNA synthetase from Mycobacterium smegmatis with bound aspartic acid
ComponentsAspartate--tRNA ligase
KeywordsLIGASE / mycobaterium / structural genomics / tRNA synthetase / AspS / AspRS / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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
ASPARTIC ACID / Aspartate--tRNA(Asp/Asn) ligase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: 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
DepositionDec 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Dec 17, 2014Group: Data collection
Revision 1.3Apr 22, 2015Group: Database references
Revision 1.4Sep 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 ligase
B: Aspartate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,0238
Polymers135,2682
Non-polymers7556
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-25 kcal/mol
Surface area43650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.400, 135.170, 157.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A0 - 801
2010B0 - 801

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Components

#1: Protein Aspartate--tRNA ligase / Aspartyl-tRNA synthetase / AspRS


Mass: 67633.984 Da / Num. of mol.: 2
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 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QWN3, aspartate-tRNA ligase
#2: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 59.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% PEG 3350, 0.2M Na Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→42.72 Å / Num. all: 51452 / Num. obs: 51363 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 35.5 Å2 / Rsym value: 0.072 / Net I/σ(I): 23.9
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 6 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 3761 / Rsym value: 0.499 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EQR
Resolution: 2.6→42.72 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 18.72 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24361 2559 5 %RANDOM
Rwork0.19548 ---
obs0.19785 48854 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.356 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å2-0 Å2
2--1.52 Å2-0 Å2
3----3.74 Å2
Refinement stepCycle: LAST / Resolution: 2.6→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8163 0 50 234 8447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198402
X-RAY DIFFRACTIONr_bond_other_d0.0040.027764
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.95911441
X-RAY DIFFRACTIONr_angle_other_deg1317740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12151090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.64923.069378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.733151192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5261575
X-RAY DIFFRACTIONr_chiral_restr0.0850.21262
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219774
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021959
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4492.1194385
X-RAY DIFFRACTIONr_mcbond_other1.4372.1154380
X-RAY DIFFRACTIONr_mcangle_it2.4133.1645461
X-RAY DIFFRACTIONr_mcangle_other2.4143.1655462
X-RAY DIFFRACTIONr_scbond_it1.5352.1984017
X-RAY DIFFRACTIONr_scbond_other1.5332.1984017
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3973.2565980
X-RAY DIFFRACTIONr_long_range_B_refined4.67516.8259151
X-RAY DIFFRACTIONr_long_range_B_other4.67516.8319152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27853 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 187 -
Rwork0.267 3561 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.65540.07430.77781.5665-0.73023.13220.0712-0.6350.09850.11250.05250.20630.0351-0.0785-0.12360.2943-0.0465-0.03520.07710.00120.10779.4067-14.091256.3511
20.4717-0.52590.60611.4052-2.13266.15420.0413-0.13160.03820.0936-0.001-0.0632-0.136-0.0875-0.04030.2236-0.03460.00170.0794-0.02160.09793.32112.322935.3839
34.6528-0.89511.61081.7617-1.67014.9708-0.0013-0.09670.13690.0074-0.0752-0.1878-0.12850.39390.07650.2050.02180.03440.0598-0.02360.093102.15097.685318.3382
40.89791.00950.31964.10621.4051.16560.0585-0.1170.11530.2786-0.0131-0.27580.03760.2996-0.04550.2090.0267-0.04230.1905-0.03490.149793.169636.489134.1803
51.0030.0635-1.19621.36990.22394.49660.1045-0.0180.3132-0.18110.0309-0.2287-0.38630.5322-0.13540.19110.00570.01320.12730.00610.195799.874520.61212.8057
610.2649-2.2073-0.82431.2408-0.17411.20910.0374-0.06340.083-0.0368-0.0994-0.47110.05880.5380.0620.27850.0071-0.02250.25450.00060.2923109.38491.116336.0942
75.02530.00010.71741.6364-0.64674.9983-0.01120.0962-0.0299-0.16580.04730.30250.1148-0.9496-0.03610.25280.0066-0.01750.24-0.00550.063583.308510.9295-10.9045
81.52770.8212-0.79021.8109-1.97945.8847-0.00260.2467-0.1214-0.2777-0.0089-0.08721.167-0.02460.01160.4090.0382-0.03480.0617-0.0360.088894.4426-3.949114.2665
94.46731.7267-1.34922.5948-1.76784.426-0.00420.0238-0.2172-0.2437-0.1693-0.27210.77430.40710.17350.37480.1242-0.04230.0558-0.00380.0616102.461-6.855229.5727
102.593-1.09070.13963.0886-0.36143.95670.28190.2199-0.5244-0.462-0.1879-0.07151.88630.2164-0.0941.411-0.0067-0.11330.0816-0.05760.228193.7252-29.200817.3422
111.0411-0.67633.06131.4351-1.512210.09790.18480.1079-0.102-0.3849-0.0042-0.36311.20610.6317-0.18071.03740.20750.1440.11830.07890.5193103.2896-25.910431.0135
120.9277-0.37390.00260.5838-1.02273.14930.12270.03690.0092-0.208-0.2544-0.17320.63150.87720.13170.52540.1225-0.01460.2771-0.0180.1681105.4161-10.117228.0574
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 101
2X-RAY DIFFRACTION2A102 - 169
3X-RAY DIFFRACTION3A170 - 237
4X-RAY DIFFRACTION4A238 - 447
5X-RAY DIFFRACTION5A448 - 544
6X-RAY DIFFRACTION6A545 - 580
7X-RAY DIFFRACTION7B2 - 110
8X-RAY DIFFRACTION8B111 - 169
9X-RAY DIFFRACTION9B170 - 237
10X-RAY DIFFRACTION10B238 - 429
11X-RAY DIFFRACTION11B430 - 486
12X-RAY DIFFRACTION12B487 - 580

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