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- PDB-3m4p: Entamoeba histolytica asparaginyl-tRNA synthetase (AsnRS) in comp... -

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Basic information

Entry
Database: PDB / ID: 3m4p
TitleEntamoeba histolytica asparaginyl-tRNA synthetase (AsnRS) in complex with asparaginyl-adenylate
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
Chem-4AD / asparagine--tRNA ligase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.83 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. / 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 ...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_ncs_dom_lim / 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_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 / _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: Asparaginyl-tRNA synthetase, putative
B: Asparaginyl-tRNA synthetase, putative
C: Asparaginyl-tRNA synthetase, putative
D: Asparaginyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,21122
Polymers210,0254
Non-polymers3,18618
Water362
1
A: Asparaginyl-tRNA synthetase, putative
B: Asparaginyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,60611
Polymers105,0122
Non-polymers1,5939
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-118 kcal/mol
Surface area35340 Å2
MethodPISA
2
C: Asparaginyl-tRNA synthetase, putative
D: Asparaginyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,60611
Polymers105,0122
Non-polymers1,5939
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11160 Å2
ΔGint-111 kcal/mol
Surface area35340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.426, 58.816, 181.259
Angle α, β, γ (deg.)90.000, 90.450, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALVALVALAA14 - 5919 - 64
21VALVALVALVALBB14 - 5919 - 64
31VALVALVALVALCC14 - 5919 - 64
41VALVALVALVALDD14 - 5919 - 64
12LEULEULEULEUAA74 - 8679 - 91
22LEULEULEULEUBB74 - 8679 - 91
32LEULEULEULEUCC74 - 8679 - 91
42LEULEULEULEUDD74 - 8679 - 91
13ILEILEILEILEAA98 - 178103 - 183
23ILEILEILEILEBB98 - 178103 - 183
33ILEILEILEILECC98 - 178103 - 183
43ILEILEILEILEDD98 - 178103 - 183
14LEULEUTYRTYRAA201 - 226206 - 231
24LEULEUTYRTYRBB201 - 226206 - 231
34LEULEUTYRTYRCC201 - 226206 - 231
44LEULEUTYRTYRDD201 - 226206 - 231
15LEULEUHISHISAA237 - 274242 - 279
25LEULEUHISHISBB237 - 274242 - 279
35LEULEUHISHISCC237 - 274242 - 279
45LEULEUHISHISDD237 - 274242 - 279
16METMETVALVALAA330 - 355335 - 360
26METMETVALVALBB330 - 355335 - 360
36METMETVALVALCC330 - 355335 - 360
46METMETVALVALDD330 - 355335 - 360
17GLUGLUGLUGLUAA363 - 387368 - 392
27GLUGLUGLUGLUBB363 - 387368 - 392
37GLUGLUGLUGLUCC363 - 387368 - 392
47GLUGLUGLUGLUDD363 - 387368 - 392
18TYRTYRPROPROAA403 - 451408 - 456
28TYRTYRPROPROBB403 - 451408 - 456
38TYRTYRPROPROCC403 - 451408 - 456
48TYRTYRPROPRODD403 - 451408 - 456

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Components

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


Mass: 52506.246 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-4AD / 4-AMINO-1,4-DIOXOBUTAN-2-AMINIUM ADENOSINE-5'-MONOPHOSPHATE / ASNAMP


Mass: 462.332 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H21N7O9P
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 ul 22 mg/ml protein in SGPP buffer mixed with 1 ul well soln. (100 mM Bis-Tris pH 5.5, 28% PEG 3350, 240 mM ammonium sulfate), drop supplemented with 10 mM L-asparagine + 10 mM ATP + 10 mM ...Details: 1 ul 22 mg/ml protein in SGPP buffer mixed with 1 ul well soln. (100 mM Bis-Tris pH 5.5, 28% PEG 3350, 240 mM ammonium sulfate), drop supplemented with 10 mM L-asparagine + 10 mM ATP + 10 mM MgCl2 + 5 mM DTT; cryoprotected by quick dip in well soln containing 30% PEG 3350 and supplemented with 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 6, 2009
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.83→50 Å / Num. obs: 50783 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Biso Wilson estimate: 73 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.058 / Net I/σ(I): 14.9
Reflection shellResolution: 2.83→2.93 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.7 / Num. unique all: 5048 / Χ2: 1.1 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.7 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.83 Å42.14 Å
Translation2.83 Å42.14 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: 1x56, protein only model prepared using CHAINSAW

1x56


Resolution: 2.83→41.36 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 1 / SU B: 33.612 / SU ML: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2577 5.1 %RANDOM
Rwork0.199 ---
obs0.202 50772 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 173.66 Å2 / Biso mean: 75.533 Å2 / Biso min: 29.97 Å2
Baniso -1Baniso -2Baniso -3
1-4.52 Å20 Å2-1.73 Å2
2--0.19 Å20 Å2
3----4.73 Å2
Refinement stepCycle: LAST / Resolution: 2.83→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13902 0 196 2 14100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02214450
X-RAY DIFFRACTIONr_bond_other_d0.0010.029793
X-RAY DIFFRACTIONr_angle_refined_deg0.9851.97719620
X-RAY DIFFRACTIONr_angle_other_deg0.7723.00123765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65151725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16523.884672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71152422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7631584
X-RAY DIFFRACTIONr_chiral_restr0.0580.22104
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115888
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022900
X-RAY DIFFRACTIONr_mcbond_it0.90248677
X-RAY DIFFRACTIONr_mcbond_other0.2443475
X-RAY DIFFRACTIONr_mcangle_it1.641614021
X-RAY DIFFRACTIONr_scbond_it1.79665773
X-RAY DIFFRACTIONr_scangle_it2.884105599
Refine LS restraints NCS

Ens-ID: 1 / Number: 4111 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.30.5
2BMEDIUM POSITIONAL0.30.5
3CMEDIUM POSITIONAL0.270.5
4DMEDIUM POSITIONAL0.310.5
1AMEDIUM THERMAL0.342
2BMEDIUM THERMAL0.352
3CMEDIUM THERMAL0.322
4DMEDIUM THERMAL0.342
LS refinement shellResolution: 2.827→2.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 175 -
Rwork0.248 3440 -
all-3615 -
obs--97.41 %
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)
11.03610.5070.24812.35111.06884.6476-0.15120.23260.2451-0.63240.3224-0.131-0.08360.5205-0.17120.0997-0.07210.05520.2550.06410.238238.68456.257570.3377
20.52460.22530.1291.86381.16994.8190.0141-0.180.08-0.1425-0.03690.61020.7425-0.85940.02280.1784-0.2131-0.06060.32630.05480.321218.4438-6.421777.9657
31.94610.4206-0.67971.8035-0.65893.1961-0.04290.1870.2123-0.22490.21890.3369-0.3654-0.6146-0.17610.3594-0.0099-0.07780.16080.0280.1619-14.649127.478518.7607
43.28560.4493-0.21661.8406-0.57773.36080.0064-0.3618-0.0960.34910.0383-0.2510.10430.3373-0.04470.3229-0.0385-0.09490.0733-0.02050.11950.183118.562236.412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 480
2X-RAY DIFFRACTION2B1 - 480
3X-RAY DIFFRACTION3C1 - 480
4X-RAY DIFFRACTION4D1 - 480

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