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- PDB-3m4q: Entamoeba histolytica asparaginyl-tRNA synthetase (AsnRS) -

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Basic information

Entry
Database: PDB / ID: 3m4q
TitleEntamoeba histolytica asparaginyl-tRNA synthetase (AsnRS)
ComponentsAsparaginyl-tRNA synthetase, putative
KeywordsLIGASE / aminoacyl-tRNA synthetase / tRNA ligase / AARS / AsnRS / translation / ATP-binding / nucleotide-binding / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP / Protein biosynthesis
Function / homology
Function and homology information


asparagine-tRNA ligase / asparagine-tRNA ligase activity / asparaginyl-tRNA aminoacylation / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
Asparagine-tRNA ligase / 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. ...Asparagine-tRNA ligase / 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. / 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
asparagine--tRNA ligase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsLarson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: to be published
Title: X-ray crystal structure of asparaginyl-tRNA synthetase from the eukaryotic human pathogen Entamoeba histolytica.
Authors: Larson, E.T. / Kim, J.E. / Zhang, L. / Napuli, A. / Kelley, A. / Castaneda, L. / Verlinde, C.L.M.J. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Hol, W.G.J. / Merritt, E.A.
History
DepositionMar 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Asparaginyl-tRNA synthetase, putative
B: Asparaginyl-tRNA synthetase, putative


Theoretical massNumber of molelcules
Total (without water)105,0122
Polymers105,0122
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-36 kcal/mol
Surface area35340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.047, 102.047, 205.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112B1 - 124
2112A1 - 124
1212B132 - 500
2212A132 - 500

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Components

#1: Protein Asparaginyl-tRNA synthetase, putative / EhAsnRS


Mass: 52506.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: 159.m00096, EHI_126920 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4LWW8, asparagine-tRNA ligase

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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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.2 ul 29 mg/ml protein in SGPP buffer mixed with 0.2 ul well soln. (100 mM HEPES pH 7.6, 25% PEG 3350, 200 mM MgCl2); cryoprotected by soaking ~1 min. in well soln supplemented with 10% PEG ...Details: 0.2 ul 29 mg/ml protein in SGPP buffer mixed with 0.2 ul well soln. (100 mM HEPES pH 7.6, 25% PEG 3350, 200 mM MgCl2); cryoprotected by soaking ~1 min. in well soln supplemented with 10% PEG 200, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 28, 2008
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 22471 / % possible obs: 99.8 % / Observed criterion σ(I): 5 / Redundancy: 13.9 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.121 / Χ2: 1.03 / Net I/σ(I): 9.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.75 / Num. unique all: 2174 / Χ2: 1.049 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.43 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.85 Å45.8 Å
Translation2.85 Å45.8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefmac_5.5.0106refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3m4p; A chain, protein only model

3m4p


Resolution: 3→45.8 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 1 / SU B: 48.301 / SU ML: 0.395 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.459 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1144 5.1 %RANDOM
Rwork0.22 ---
obs0.222 22380 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 161.19 Å2 / Biso mean: 87.156 Å2 / Biso min: 47.67 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å20 Å20 Å2
2--3.41 Å20 Å2
3----6.82 Å2
Refinement stepCycle: LAST / Resolution: 3→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6742 0 0 0 6742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226919
X-RAY DIFFRACTIONr_bond_other_d0.0010.024617
X-RAY DIFFRACTIONr_angle_refined_deg0.9581.9589406
X-RAY DIFFRACTIONr_angle_other_deg0.765311236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4945861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96623.681307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3041537
X-RAY DIFFRACTIONr_chiral_restr0.0560.21019
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217763
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021422
X-RAY DIFFRACTIONr_mcbond_it0.75444323
X-RAY DIFFRACTIONr_mcbond_other0.241737
X-RAY DIFFRACTIONr_mcangle_it1.34966917
X-RAY DIFFRACTIONr_scbond_it1.47562596
X-RAY DIFFRACTIONr_scangle_it2.376102489
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
2474TIGHT POSITIONAL0.270.05
2916MEDIUM POSITIONAL0.340.5
2474TIGHT THERMAL0.280.5
2916MEDIUM THERMAL0.272
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 73 -
Rwork0.293 1507 -
all-1580 -
obs--98.01 %
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)
12.77911.04450.69832.14490.57442.70530.0705-0.1071-0.30250.09630.0776-0.23340.91830.3081-0.14810.37650.11050.01950.33820.07770.113210.098747.1844-11.9581
23.45480.14751.29781.210.00032.89080.0524-0.4090.49970.253-0.09440.3539-0.2949-0.41160.0420.16230.03330.10150.3979-0.00620.3198-1.728767.366-5.5985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 500
2X-RAY DIFFRACTION2B1 - 500

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