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- PDB-2cx5: Crystal structure of a putative trans-editing enzyme for prolyl t... -

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Basic information

Entry
Database: PDB / ID: 2cx5
TitleCrystal structure of a putative trans-editing enzyme for prolyl tRNA synthetase
ComponentsA PUTATIVE TRANS-EDITING ENZYME
KeywordsTRANSLATION / trans-editing domain / prolyl-tRNA synthetase / RSGI / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative
Function / homologyYbaK protein / YbaK/aminoacyl-tRNA synthetase-associated domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / aminoacyl-tRNA deacylase activity / Alpha-Beta Complex / Alpha Beta / YbaK/aminoacyl-tRNA synthetase-associated domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMurayama, K. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of a putative trans-editing enzyme for prolyl tRNA synthetase
Authors: Murayama, K. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 28, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2005Provider: 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A PUTATIVE TRANS-EDITING ENZYME
B: A PUTATIVE TRANS-EDITING ENZYME
C: A PUTATIVE TRANS-EDITING ENZYME
D: A PUTATIVE TRANS-EDITING ENZYME


Theoretical massNumber of molelcules
Total (without water)66,3004
Polymers66,3004
Non-polymers00
Water9,422523
1
A: A PUTATIVE TRANS-EDITING ENZYME


Theoretical massNumber of molelcules
Total (without water)16,5751
Polymers16,5751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: A PUTATIVE TRANS-EDITING ENZYME


Theoretical massNumber of molelcules
Total (without water)16,5751
Polymers16,5751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: A PUTATIVE TRANS-EDITING ENZYME


Theoretical massNumber of molelcules
Total (without water)16,5751
Polymers16,5751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: A PUTATIVE TRANS-EDITING ENZYME


Theoretical massNumber of molelcules
Total (without water)16,5751
Polymers16,5751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.576, 61.245, 84.186
Angle α, β, γ (deg.)90.00, 110.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
A PUTATIVE TRANS-EDITING ENZYME


Mass: 16575.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHN1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% PEG400, 2.0M Ammonium sulphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 21, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 46278 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 12.8 Å2 / Rsym value: 0.062 / Net I/σ(I): 22.2
Reflection shellResolution: 1.9→1.97 Å / Rsym value: 0.268

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→8.74 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1678470.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2292 5 %RANDOM
Rwork0.197 ---
obs0.197 45761 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 78.2023 Å2 / ksol: 0.515778 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20.09 Å2
2---0.24 Å20 Å2
3---1.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→8.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4644 0 0 523 5167
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.891.5
X-RAY DIFFRACTIONc_mcangle_it2.562
X-RAY DIFFRACTIONc_scbond_it3.092
X-RAY DIFFRACTIONc_scangle_it4.332.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 409 5.4 %
Rwork0.212 7209 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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