[English] 日本語
Yorodumi
- PDB-1nj2: Crystal structure of Prolyl-tRNA Synthetase from Methanothermobac... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1nj2
TitleCrystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus
ComponentsProline-tRNA Synthetase
KeywordsLIGASE / Class-II tRNA synthetase
Function / homologyAminoacyl-tRNA synthetase, class II / Prolyl-tRNA synthetase, catalytic domain / Aminoacyl-transfer RNA synthetases class-II family profile. / Prolyl-tRNA synthetase, C-terminal / Anticodon binding domain / tRNA synthetase class II core domain (G, H, P, S and T) / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / Proline-tRNA ligase, class IIa / Anticodon-binding / Proline-tRNA ligase, class IIa, archaeal-type ...Aminoacyl-tRNA synthetase, class II / Prolyl-tRNA synthetase, catalytic domain / Aminoacyl-transfer RNA synthetases class-II family profile. / Prolyl-tRNA synthetase, C-terminal / Anticodon binding domain / tRNA synthetase class II core domain (G, H, P, S and T) / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / Proline-tRNA ligase, class IIa / Anticodon-binding / Proline-tRNA ligase, class IIa, archaeal-type / Anticodon-binding domain superfamily / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, class II / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / ATP binding / metal ion binding / cytoplasm / Proline--tRNA ligase
Function and homology information
Specimen sourceMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.11 Å resolution
AuthorsKamtekar, S. / Kennedy, W.D. / Wang, J. / Stathopoulos, C. / Soll, D. / Steitz, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases
Authors: Kamtekar, S. / Kennedy, W.D. / Wang, J. / Stathopoulos, C. / Soll, D. / Steitz, T.A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 30, 2002 / Release: Mar 4, 2003
RevisionDateData content typeGroupProviderType
1.0Mar 4, 2003Structure modelrepositoryInitial release
1.1Apr 29, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Source and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proline-tRNA Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2603
Polyers58,1701
Non-polymers902
Water23413
1
A: Proline-tRNA Synthetase
hetero molecules

A: Proline-tRNA Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5206
Polyers116,3412
Non-polymers1794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area (Å2)4510
ΔGint (kcal/M)-50
Surface area (Å2)41670
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)145.077, 145.077, 170.359
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP 65 2 2
DetailsThe biological assembly is a dimer constructed by a twofold rotation.

-
Components

#1: Protein/peptide Proline-tRNA Synthetase / E.C.6.1.1.15 / Prolyl-tRNA synthetase / Proline--tRNA ligase / ProRS


Mass: 58170.258 Da / Num. of mol.: 1 / Fragment: N terminally His Tagged Enzyme
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Genus: Methanothermobacter
Species: Methanothermobacter thermautotrophicusMethanothermobacter
Strain: Delta H
Description: Strain supplemented with additional plasmid encoding rare tRNAs
Gene: MTH611 / Plasmid name: pET15b / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 RecA- / References: UniProt: O26708, proline-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.98 / Density percent sol: 75.13 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris, Beta-Mercaptoethanol, MgCl2,NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temp: 12-25 ℃ / pH: 8.5 / Method: vapor diffusion
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDDetailsChemical formula
15 mg/mlproteindrop
220 mMTrisdroppH8.5
3200 mMdropNaCl
45 mM2-mercaptoethanoldrop
50.2 Mammonium sulfatereservoir
620-30 %PEG4000reservoir
75 mM2-mercaptoethanolreservoir
80.1 MreservoirpH4.5NaOAc

-
Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: CHESS BEAMLINE A1 / Synchrotron site: CHESS / Beamline: A1 / Wavelength: 0.945
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: Dec 20, 2000
RadiationMonochromator: Si(111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.945 Å / Relative weight: 1
ReflectionD resolution high: 3.1 Å / D resolution low: 3 Å / Number all: 36062 / Number obs: 35918 / Observed criterion sigma I: -3 / Rmerge I obs: 0.066 / NetI over sigmaI: 22.8 / Redundancy: 4.7 % / Percent possible obs: 99.6
Reflection shellRmerge I obs: 0.77 / Highest resolution: 3.1 Å / Lowest resolution: 3.21 Å / MeanI over sigI obs: 2 / Percent possible all: 99.7
Reflection
*PLUS
D resolution high: 3.1 Å
Reflection shell
*PLUS
Percent possible obs: 99.7

+
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.0refinement
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Methanocaldococcus janaschii Proline tRNA Synthetase

R Free selection details: RANDOM / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 24.3074 / Solvent model param ksol: 0.264032
Displacement parametersB iso mean: 89.4 Å2 / Aniso B11: 7.03 Å2 / Aniso B12: 14.95 Å2 / Aniso B13: 0 Å2 / Aniso B22: 7.03 Å2 / Aniso B23: 0 Å2 / Aniso B33: -14.06 Å2
Least-squares processR factor R free: 0.273 / R factor R free error: 0.005 / R factor R work: 0.239 / R factor all: 0.239 / R factor obs: 0.239 / Highest resolution: 3.11 Å / Lowest resolution: 29.95 Å / Number reflection R free: 3457 / Number reflection all: 36056 / Number reflection obs: 34613 / Percent reflection R free: 1 / Percent reflection obs: 96
Refine analyzeLuzzati coordinate error free: 0.52 Å / Luzzati sigma a free: 0.75 Å
Refine hist #LASTHighest resolution: 3.11 Å / Lowest resolution: 29.95 Å
Number of atoms included #LASTProtein: 3693 / Nucleic acid: 0 / Ligand: 2 / Solvent: 13 / Total: 3708
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.611.50
X-RAY DIFFRACTIONc_mcangle_it2.922.00
X-RAY DIFFRACTIONc_scbond_it2.232.00
X-RAY DIFFRACTIONc_scangle_it3.772.50
Refine LS shellHighest resolution: 3.11 Å / R factor R free: 0.387 / R factor R free error: 0.018 / R factor R work: 0.366 / Lowest resolution: 3.29 Å / Number reflection R free: 479 / Number reflection R work: 4549 / Total number of bins used: 6 / Percent reflection R free: 9.5 / Percent reflection obs: 82.6
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Least-squares process
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3 Å
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more