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- PDB-2e1b: Crystal structure of the AlaX-M trans-editing enzyme from Pyrococ... -

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Basic information

Entry
Database: PDB / ID: 2e1b
TitleCrystal structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii
Components216aa long hypothetical alanyl-tRNA synthetase
KeywordsLIGASE / HYDROLASE / zinc-binding motif / trans-editing enzyme / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / nucleic acid binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #130 / : / Threonyl-trna Synthetase; Chain A, domain 2 / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl-tRNA Synthetase; Chain A, domain 2 / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, SAD ...Elongation Factor Tu (Ef-tu); domain 3 - #130 / : / Threonyl-trna Synthetase; Chain A, domain 2 / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl-tRNA Synthetase; Chain A, domain 2 / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Translation protein, beta-barrel domain superfamily / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Alanyl-tRNA editing protein AlaX-M
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsFukunaga, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007
Title: Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii
Authors: Fukunaga, R. / Yokoyama, S.
History
DepositionOct 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: 216aa long hypothetical alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4042
Polymers25,3391
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.223, 80.223, 72.269
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein 216aa long hypothetical alanyl-tRNA synthetase / PH0108


Mass: 25338.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O57848, alanine-tRNA ligase, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100mM Bicine-NaOH buffer (pH 9.0), 22% PEG6000, 0.1M ammoniumacetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL41XU20.9793, 0.9796, 0.9643, 0.9953
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 27, 2006
ADSC QUANTUM 3152CCDNov 10, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97931
30.97961
40.96431
50.99531
ReflectionResolution: 2.7→50 Å / Num. all: 7338 / Num. obs: 7167 / % possible obs: 97.7 % / Redundancy: 7.8 % / Biso Wilson estimate: 56.3 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 34.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2 / Num. unique all: 647 / Rsym value: 0.34 / % possible all: 90.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→40.11 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1170548.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.313 781 10.9 %RANDOM
Rwork0.227 ---
obs0.227 7167 97.6 %-
all-7338 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.1543 Å2 / ksol: 0.265579 e/Å3
Displacement parametersBiso mean: 82.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.46 Å219.62 Å20 Å2
2--6.46 Å20 Å2
3----12.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.7→40.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 1 0 1787
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it6.231.5
X-RAY DIFFRACTIONc_mcangle_it92
X-RAY DIFFRACTIONc_scbond_it8.522
X-RAY DIFFRACTIONc_scangle_it10.962.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 117 10.5 %
Rwork0.321 993 -
obs--92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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