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- PDB-3i7f: Aspartyl tRNA synthetase from Entamoeba histolytica -

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Basic information

Entry
Database: PDB / ID: 3i7f
TitleAspartyl tRNA synthetase from Entamoeba histolytica
ComponentsAspartyl-tRNA synthetase
KeywordsLIGASE / tRNA ligase / apo / ATP-binding / Aminoacyl-tRNA synthetase / Nucleotide-binding / Protein biosynthesis / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / RNA binding / ATP binding / cytosol
Similarity search - Function
Aspartate-tRNA synthetase, type 2 / 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. ...Aspartate-tRNA synthetase, type 2 / 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. / 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
Aspartyl-tRNA synthetase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsArakaki, T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2010
Title: Crystal structure of the aspartyl-tRNA synthetase from Entamoeba histolytica.
Authors: Merritt, E.A. / Arakaki, T.L. / Larson, E.T. / Kelley, A. / Mueller, N. / Napuli, A.J. / Zhang, L. / Deditta, G. / Luft, J. / Verlinde, C.L. / Fan, E. / Zucker, F. / Buckner, F.S. / Van Voorhis, W.C. / Hol, W.G.
History
DepositionJul 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartyl-tRNA synthetase
B: Aspartyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)125,9512
Polymers125,9512
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-47.6 kcal/mol
Surface area40840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)247.848, 247.848, 56.295
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNSERSER2AA27 - 16531 - 169
21ASNASNSERSER2BB27 - 16531 - 169
12GLNGLNMETMET2AA220 - 397224 - 401
22GLNGLNMETMET2BB220 - 397224 - 401
13VALVALARGARG2AA417 - 541421 - 545
23VALVALARGARG2BB417 - 541421 - 545
14LEULEUGLUGLU3AA398 - 416402 - 420
24LEULEUGLUGLU3BB398 - 416402 - 420
15GLNGLNGLUGLU3AA10 - 2614 - 30
25GLNGLNGLUGLU3BB10 - 2614 - 30
16VALVALLYSLYS3AA166 - 176170 - 180
26VALVALLYSLYS3BB166 - 176170 - 180

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Aspartyl-tRNA synthetase


Mass: 62975.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: cleaved / Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_175050 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4LZN0*PLUS, aspartate-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 0.2 M Lithium sulfate, 0.1 M Bis-Tris pH 5.5, 23% PEG 3350, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.851
11K, H, -L20.149
ReflectionResolution: 2.8→50 Å / Num. obs: 31605 / % possible obs: 99.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.1 / Χ2: 1.152 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.94.80.73530621.072197.6
2.9-3.025.90.56931711.057199.6
3.02-3.156.40.39831891.0951100
3.15-3.326.50.28331581.1031100
3.32-3.536.50.19631971.2491100
3.53-3.86.50.13431551.3541100
3.8-4.186.50.09231491.191100
4.18-4.796.50.07231991.2931100
4.79-6.036.50.06331681.1351100
6.03-506.40.03631570.921199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.815 / SU B: 51.924 / SU ML: 0.413 / SU R Cruickshank DPI: 0.062 / SU Rfree: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1641 5.2 %RANDOM
Rwork0.2 ---
obs0.202 31597 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.47 Å2 / Biso mean: 19.509 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--11.47 Å20 Å20 Å2
2---11.47 Å20 Å2
3---22.94 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7659 0 0 78 7737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227827
X-RAY DIFFRACTIONr_bond_other_d0.0020.025360
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.97510612
X-RAY DIFFRACTIONr_angle_other_deg0.903313073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95323.868349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.422151345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0551550
X-RAY DIFFRACTIONr_chiral_restr0.0760.21204
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218618
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021594
X-RAY DIFFRACTIONr_mcbond_it0.3511.54852
X-RAY DIFFRACTIONr_mcbond_other0.0881.51918
X-RAY DIFFRACTIONr_mcangle_it0.69627885
X-RAY DIFFRACTIONr_scbond_it1.25632975
X-RAY DIFFRACTIONr_scangle_it2.0914.52727
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1822TIGHT POSITIONAL0.030.05
1959MEDIUM POSITIONAL0.030.5
1822TIGHT THERMAL0.060.5
1959MEDIUM THERMAL0.082
2937TIGHT POSITIONAL0.030.05
21318MEDIUM POSITIONAL0.030.5
2937TIGHT THERMAL0.080.5
21318MEDIUM THERMAL0.082
3731TIGHT POSITIONAL0.030.05
3969MEDIUM POSITIONAL0.030.5
3731TIGHT THERMAL0.070.5
3969MEDIUM THERMAL0.092
4111TIGHT POSITIONAL0.030.05
4119LOOSE POSITIONAL0.035
4111TIGHT THERMAL0.070.5
4119LOOSE THERMAL0.110
597TIGHT POSITIONAL0.030.05
587LOOSE POSITIONAL0.045
597TIGHT THERMAL0.050.5
587LOOSE THERMAL0.0710
666TIGHT POSITIONAL0.020.05
648LOOSE POSITIONAL0.035
666TIGHT THERMAL0.030.5
648LOOSE THERMAL0.0310
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 119 -
Rwork0.351 2051 -
all-2170 -
obs--93.82 %
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)
12.73160.1213-0.34512.93890.6572.04660.04360.4195-0.351-0.438-0.0365-0.16840.20580.2467-0.00710.28990.0847-0.04280.2395-0.05680.175610.766-36.073-27.85
26.5283-16.2818-6.855931.461411.4982.2884-0.354-0.4704-1.77241.0451-0.32782.2110.59170.33350.68181.78360.00240.2850.97140.06731.07554.344-62.014-22.748
34.6826-0.2890.170.7163-0.38190.0971-0.0264-0.0316-0.6820.01910.05370.29470.217-0.1279-0.02740.411-0.1305-0.0460.2092-0.09950.3878-19.698-40.996-22.251
412.4026-3.84341.35093.4752-0.07413.7710.3418-0.6906-1.91010.16840.05130.48951.14910.3298-0.3930.5763-0.1121-0.18860.32030.11690.8056-29.722-47.032-15.675
55.35920.0054-1.50880.46740.02380.88870.06220.0439-1.4816-0.09920.07450.23330.4459-0.0508-0.13670.6149-0.147-0.32620.2992-0.07591.1561-31.746-54.698-24.764
65.14761.58620.68484.1880.80732.7510.12290.32290.2432-0.2711-0.04050.6024-0.0471-0.6336-0.08240.2751-0.0916-0.10790.56940.16770.6535-59.544-32.505-22.057
7-3.33772.8612-1.17145.25477.68173.08280.7863-0.82510.36820.9384-0.8656-0.62680.237-0.17010.07930.9911-0.370.31271.58520.31681.1318-53.128-16.813-1.433
87.0729-0.68020.28360.54690.64820.27970.1477-0.2199-0.69220.2277-0.04640.11010.2441-0.1585-0.10130.3134-0.1132-0.08970.13960.06980.3249-29.007-32.103-17.332
918.41-0.1424-2.53898.4524-3.60791.94570.0577-2.04840.17091.25280.32731.0151-0.13150.2981-0.3850.5023-0.01220.02950.3271-0.07790.2922-16.525-32.579-10.843
101.3943-0.57650.05320.83280.07551.04270.0186-0.2341-0.24150.11420.07780.2520.1493-0.1537-0.09640.2199-0.0725-0.00130.14990.04690.158-16.237-20.427-10.072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 170
2X-RAY DIFFRACTION2A171 - 225
3X-RAY DIFFRACTION3A226 - 268
4X-RAY DIFFRACTION4A289 - 335
5X-RAY DIFFRACTION5A336 - 544
6X-RAY DIFFRACTION6B10 - 167
7X-RAY DIFFRACTION7B168 - 224
8X-RAY DIFFRACTION8B225 - 268
9X-RAY DIFFRACTION9B289 - 338
10X-RAY DIFFRACTION10B339 - 544

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