[English] 日本語
Yorodumi
- PDB-3ial: Giardia lamblia Prolyl-tRNA synthetase in complex with prolyl-ade... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ial
TitleGiardia lamblia Prolyl-tRNA synthetase in complex with prolyl-adenylate
ComponentsProlyl-tRNA synthetase
KeywordsLIGASE / aminoacyl-tRNA synthetase / tRNA ligase / AARS / ProRS / CysRS / Pro(Cys)RS / translation / ATP-binding / nucleotide-binding / Structural Genomics / Medical Structural Genomics of Pathogenic Protazoa / MSGPP / Medical Structural Genomics of Pathogenic Protozoa
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / mitochondrion / ATP binding
Similarity search - Function
C-terminal domain of ProRS / Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Translation Initiation Factor IF3 / Anticodon-binding domain ...C-terminal domain of ProRS / Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Translation Initiation Factor IF3 / Anticodon-binding domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PR8 / Prolyl-tRNA synthetase
Similarity search - Component
Biological speciesGiardia lamblia ATCC 50803 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLarson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of the prolyl-tRNA synthetase from the eukaryotic pathogen Giardia lamblia.
Authors: Larson, E.T. / Kim, J.E. / Napuli, A.J. / Verlinde, C.L. / Fan, E. / Zucker, F.H. / Van Voorhis, W.C. / Buckner, F.S. / Hol, W.G. / Merritt, E.A.
History
DepositionJul 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prolyl-tRNA synthetase
B: Prolyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,46110
Polymers117,0202
Non-polymers1,4418
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-30 kcal/mol
Surface area39690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.338, 87.624, 142.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Prolyl-tRNA synthetase


Mass: 58509.992 Da / Num. of mol.: 2 / Fragment: ProRS (amino acids 34-542)
Source method: isolated from a genetically manipulated source
Details: residues 1-33 were replaced with a non-cleavable His tag during cloning
Source: (gene. exp.) Giardia lamblia ATCC 50803 (eukaryote) / Gene: GL50803_15983, ProRS / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8BR89, proline-tRNA ligase
#2: Chemical ChemComp-PR8 / 5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2-ylcarbonyl]oxy}phosphoryl]adenosine / prolyl-adenylate


Mass: 444.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21N6O8P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 7.8
Details: 28% PEG 3350, 0.21 M MgCl2, 0.1 M Tris-HCl (pH 7.8), 10 mM ATP, 10 mM L-Proline, 1 mM TCEP; for cryoprotection, crystal-containing drop was diluted approx. four-fold with 30% glycerol, 0.175 ...Details: 28% PEG 3350, 0.21 M MgCl2, 0.1 M Tris-HCl (pH 7.8), 10 mM ATP, 10 mM L-Proline, 1 mM TCEP; for cryoprotection, crystal-containing drop was diluted approx. four-fold with 30% glycerol, 0.175 M MgCl2, 24.5% PEG 3350, 0.105 M Tris (pH 8.2), 0.7 mM TCEP and crystal was frozen in LN2 after several minutes of equilibration., sitting drop vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MarUSA MarMosaic -325 CCD / Detector: CCD / Date: Dec 8, 2008
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 52868 / % possible obs: 98.7 % / Observed criterion σ(I): 5 / Redundancy: 4.5 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1.031 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.8 / Num. unique all: 4857 / Χ2: 1.025 / % possible all: 92.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.79 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.19 Å
Translation2.5 Å30.19 Å

-
Processing

Software
NameVersionClassificationNB
HKL-2000data scaling
PHASER2.1.4phasing
REFMACrefmac_5.5.0096refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NJ5

1nj5


Resolution: 2.2→30.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 11.772 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES ARE RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2726 5.2 %RANDOM
Rwork0.172 ---
obs0.174 52791 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 88.98 Å2 / Biso mean: 34.624 Å2 / Biso min: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20 Å2
2---0.1 Å20 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7924 0 96 215 8235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228238
X-RAY DIFFRACTIONr_bond_other_d0.0010.025712
X-RAY DIFFRACTIONr_angle_refined_deg1.071.97111142
X-RAY DIFFRACTIONr_angle_other_deg0.7983.00113880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8951002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.36523.913368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.427151452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5061552
X-RAY DIFFRACTIONr_chiral_restr0.0620.21231
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021652
X-RAY DIFFRACTIONr_mcbond_it1.33445012
X-RAY DIFFRACTIONr_mcbond_other0.36642024
X-RAY DIFFRACTIONr_mcangle_it2.2368127
X-RAY DIFFRACTIONr_scbond_it2.74163226
X-RAY DIFFRACTIONr_scangle_it4.163103013
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 197 -
Rwork0.205 3318 -
all-3515 -
obs--90.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1525-0.101-0.07520.73060.16350.98750.0195-0.0872-0.13720.0651-0.02270.02630.1363-0.09810.00330.1398-0.0310.00210.1480.00220.176861.253782.78413.8709
20.9710.0702-0.18870.56450.08430.68650.0586-0.05230.09040.0482-0.00220.0274-0.0155-0.0802-0.05640.1415-0.0027-0.00140.166-0.01510.164753.97290.35496.1686
32.92960.542-0.87811.3185-0.54911.23160.01820.46730.2503-0.18230.0615-0.1325-0.0980.0381-0.07970.1223-0.01550.02840.19440.03210.080370.205895.8168-19.5135
41.4108-0.0697-0.32551.00710.09362.10360.0130.0237-0.09080.0205-0.0570.02060.1801-0.09230.0440.1167-0.0301-0.00540.1182-0.0280.132133.590379.66292.0461
50.6188-0.0692-0.01110.68720.32761.03050.0017-0.0848-0.11740.1209-0.02640.00520.1345-0.02050.02470.1652-0.0022-0.01310.13930.01170.171677.270284.889718.1086
60.5968-0.13290.12850.78080.51531.08130.0021-0.0103-0.08890.05680.0136-0.02650.10510.121-0.01570.1353-0.0011-0.00350.12180.00180.148989.165687.985714.6461
71.2698-0.19390.18141.5532-0.46122.08720.00330.00640.1176-0.0046-0.02730.1246-0.4493-0.19940.0240.22560.0567-0.01470.0786-0.02640.153468.6131121.851817.1037
81.7793-1.60650.59161.9172-0.56110.81340.01710.08450.1371-0.0479-0.0467-0.1088-0.0250.1750.02960.1153-0.0441-0.00490.1226-0.00070.1224100.393898.076624.0755
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 203
2X-RAY DIFFRACTION2A204 - 342
3X-RAY DIFFRACTION3A343 - 456
4X-RAY DIFFRACTION4A457 - 542
5X-RAY DIFFRACTION5B38 - 178
6X-RAY DIFFRACTION6B179 - 315
7X-RAY DIFFRACTION7B316 - 433
8X-RAY DIFFRACTION8B434 - 542

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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