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- PDB-1wxo: Structure of Archaeal Trans-Editing Protein AlaX in complex with zinc -

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Basic information

Entry
Database: PDB / ID: 1wxo
TitleStructure of Archaeal Trans-Editing Protein AlaX in complex with zinc
Componentsalanyl-tRNA synthetaseAlanine—tRNA ligase
KeywordsHYDROLASE / Trans-editing
Function / homology
Function and homology information


aminoacyl-tRNA editing activity / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Replication Terminator Protein; Chain A, domain 2 - #20 / Threonyl-trna Synthetase; Chain A, domain 2 / Replication Terminator Protein; Chain A, domain 2 / Threonyl-tRNA Synthetase; Chain A, domain 2 / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alanyl-tRNA editing protein AlaX-S
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsSokabe, M. / Okada, A. / Nakashima, T. / Yao, M. / Tanaka, I.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Molecular basis of alanine discrimination in editing site
Authors: Sokabe, M. / Okada, A. / Yao, M. / Nakashima, T. / Tanaka, I.
History
DepositionJan 27, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

Downloads & links

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Assembly

Deposited unit
A: alanyl-tRNA synthetase
B: alanyl-tRNA synthetase
C: alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7456
Polymers54,5493
Non-polymers1963
Water7,602422
1
A: alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2482
Polymers18,1831
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2482
Polymers18,1831
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2482
Polymers18,1831
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.472, 97.971, 60.584
Angle α, β, γ (deg.)90.00, 95.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alanyl-tRNA synthetase / Alanine—tRNA ligase / Trans-Editing Protein AlaX


Mass: 18183.059 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0574 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codonplus-(DE3)-RIL-X / References: UniProt: O58307
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.3 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG8000, MES-Na, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2004 / Details: mirror
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 39904 / Num. obs: 39904 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.1
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3962 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V7O

1v7o


Resolution: 1.88→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 3987 -random
Rwork0.1926 ---
all-39904 --
obs-39904 99.8 %-
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.974 Å20 Å22.121 Å2
2--1.805 Å20 Å2
3---1.169 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3737 0 3 422 4162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005028
X-RAY DIFFRACTIONc_angle_deg1.33578
X-RAY DIFFRACTIONc_dihedral_angle_d23.15005
X-RAY DIFFRACTIONc_improper_angle_d0.78524
LS refinement shellResolution: 1.88→1.89 Å
RfactorNum. reflection
Rfree0.3033 61
Rwork0.2731 -
obs-649

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