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- PDB-2cwp: Crystal structure of MetRS related protein from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 2cwp
TitleCrystal structure of MetRS related protein from Pyrococcus horikoshii
ComponentsMetRS related protein
KeywordsLIGASE / MetRS related protein / Pyrococcus horikoshii / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
: / Methionyl-tRNA synthetase, beta subunit, C-terminal / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Methionine--tRNA ligase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of MetRS related protein from Pyrococcus horikoshii
Authors: Murayama, K. / Kato-Murayama, M. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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: MetRS related protein


Theoretical massNumber of molelcules
Total (without water)12,9051
Polymers12,9051
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MetRS related protein

A: MetRS related protein


Theoretical massNumber of molelcules
Total (without water)25,8102
Polymers25,8102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3400 Å2
ΔGint-30 kcal/mol
Surface area10860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.841, 50.354, 44.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein MetRS related protein


Mass: 12905.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58023
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% PEGMME2000, 5mM NiCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 21, 2005
RadiationMonochromator: conforcal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 6735 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 16.7 Å2 / Rsym value: 0.031 / Net I/σ(I): 42.5
Reflection shellResolution: 2.1→2.18 Å / Rsym value: 0.161 / % possible all: 78

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→27.61 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1158535.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 716 10.9 %RANDOM
Rwork0.214 ---
obs0.214 6597 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.5713 Å2 / ksol: 0.359573 e/Å3
Displacement parametersBiso mean: 37.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.53 Å20 Å20 Å2
2---0.63 Å20 Å2
3---6.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→27.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 0 47 927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 104 11.4 %
Rwork0.232 808 -
obs--82.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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