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- PDB-1v4p: Crystal structure of Alanyl-tRNA Synthetase from Pyrococcus horik... -

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Basic information

Entry
Database: PDB / ID: 1v4p
TitleCrystal structure of Alanyl-tRNA Synthetase from Pyrococcus horikoshii OT3
Componentsalanyl-tRNA synthetase
KeywordsLIGASE / alanyl-tRNA synthetase / alanine-tRNA ligase / Pyrococcus horikoshii / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


Ser-tRNA(Ala) hydrolase activity / 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 / MAD / Resolution: 1.45 Å
AuthorsIshijima, J. / Yutani, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of alanyl-tRNA synthetase editing-domain homolog (PH0574) from a hyperthermophile, Pyrococcus horikoshii OT3 at 1.45 A resolution
Authors: Ishijima, J. / Uchida, Y. / Kuroishi, C. / Tuzuki, C. / Takahashi, N. / Okazaki, N. / Yutani, K. / Miyano, M.
History
DepositionNov 14, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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
Water10,791599
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
MethodPISA
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
4
A: alanyl-tRNA synthetase
C: alanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4974
Polymers36,3662
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.802, 97.861, 60.872
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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Components

#1: Protein alanyl-tRNA synthetase


Mass: 18183.059 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: O58307, alanine-tRNA ligase
#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


Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.09 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.3 / Details: PEG 4000, pH 6.3, Microbatch, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B121.0, 0.9792, 0.9795
Detector
TypeIDDetectorDate
RIGAKU RAXIS V1IMAGE PLATEOct 3, 2003
RIGAKU JUPITER 2102CCDOct 31, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorSINGLE WAVELENGTHMx-ray1
2mirrorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97921
30.97951
ReflectionResolution: 1.45→50 Å / Num. all: 88112 / Num. obs: 88112 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.3 / Num. unique all: 8751 / % possible all: 99.5

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.45→38.04 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4409 -random
Rwork0.206 ---
all0.207 87972 --
obs0.207 87972 99.9 %-
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å20 Å2
2---0.47 Å20 Å2
3----1.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.45→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3724 0 3 599 4326
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.297
X-RAY DIFFRACTIONc_bond_d0.0045
LS refinement shellResolution: 1.45→1.46 Å
RfactorNum. reflection
Rfree0.3006 94
Rwork0.2795 -
obs-1680

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