[English] 日本語
Yorodumi
- PDB-4ncx: Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ncx
TitleCrystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum 3D7
ComponentsProline--tRNA ligase
KeywordsLIGASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Prolyl-tRNA synthetase
Function / homology
Function and homology information


Ala-tRNA(Pro) hydrolase activity / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / aminoacyl-tRNA synthetase multienzyme complex / ATP binding / cytoplasm
Similarity search - Function
C-terminal domain of ProRS / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / 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 ...C-terminal domain of ProRS / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / 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. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Proline--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acs Infect Dis. / Year: 2017
Title: Biochemical and Structural Characterization of Selective Allosteric Inhibitors of the Plasmodium falciparum Drug Target, Prolyl-tRNA-synthetase.
Authors: Hewitt, S.N. / Dranow, D.M. / Horst, B.G. / Abendroth, J.A. / Forte, B. / Hallyburton, I. / Jansen, C. / Baragana, B. / Choi, R. / Rivas, K.L. / Hulverson, M.A. / Dumais, M. / Edwards, T.E. ...Authors: Hewitt, S.N. / Dranow, D.M. / Horst, B.G. / Abendroth, J.A. / Forte, B. / Hallyburton, I. / Jansen, C. / Baragana, B. / Choi, R. / Rivas, K.L. / Hulverson, M.A. / Dumais, M. / Edwards, T.E. / Lorimer, D.D. / Fairlamb, A.H. / Gray, D.W. / Read, K.D. / Lehane, A.M. / Kirk, K. / Myler, P.J. / Wernimont, A. / Walpole, C. / Stacy, R. / Barrett, L.K. / Gilbert, I.H. / Van Voorhis, W.C.
History
DepositionOct 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name / _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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proline--tRNA ligase
B: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,45211
Polymers117,9732
Non-polymers4799
Water10,881604
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-35 kcal/mol
Surface area37330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.960, 91.380, 110.840
Angle α, β, γ (deg.)90.000, 129.480, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1130-

HOH

DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

-
Components

#1: Protein Proline--tRNA ligase / Prolyl-tRNA synthetase / ProRS


Mass: 58986.496 Da / Num. of mol.: 2 / Fragment: C-terimus residues 249-746
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: 3D7 / Gene: proRS, PFL0670c / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I5R7, proline-tRNA ligase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus(b2): 0.1M each MES, Imidazole, pH 6.5, 0.09M each NaF, NaBr, NaI, 30% ethylene glycol, PEG-8000 and 5mM L-Proline, 5mM ATP, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 97461 / Num. obs: 96638 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 32.393 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.36
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.90.4913.1132554709499.2
1.9-1.950.3364.5331847694299.5
1.95-2.010.2685.5330889671999.3
2.01-2.070.2077.1830465664199.4
2.07-2.140.1688.7229109634599.3
2.14-2.210.13410.6828275615299.4
2.21-2.290.10812.9527131593399.3
2.29-2.390.09314.6126220572299.4
2.39-2.490.08116.9325378553199.4
2.49-2.620.06520.1723979524899.6
2.62-2.760.05723.0222737500999.4
2.76-2.930.04826.7121480473199.3
2.93-3.130.0431.6919943445198.9
3.13-3.380.03436.8118217413399.1
3.38-3.70.03140.9916491380598.8
3.7-4.140.02944.1314831346198.7
4.14-4.780.02646.813109303898.8
4.78-5.850.02546.611157258998.4
5.85-8.270.02446.278602201998.6
8.270.02148.574294107592.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HVC

4hvc


Resolution: 1.85→46.46 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2034 / WRfactor Rwork: 0.1651 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8632 / SU B: 5.092 / SU ML: 0.079 / SU R Cruickshank DPI: 0.115 / SU Rfree: 0.1139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 4832 5 %RANDOM
Rwork0.169 ---
obs0.1709 96637 99.52 %-
all-101469 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.71 Å2 / Biso mean: 33.037 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å2-0 Å20.32 Å2
2--0.39 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7084 0 27 604 7715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197425
X-RAY DIFFRACTIONr_bond_other_d0.0010.026938
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.94410071
X-RAY DIFFRACTIONr_angle_other_deg0.833316001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70824.754345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.711151282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6761528
X-RAY DIFFRACTIONr_chiral_restr0.10.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021718
X-RAY DIFFRACTIONr_mcbond_it1.441.8983586
X-RAY DIFFRACTIONr_mcbond_other1.4371.8973585
X-RAY DIFFRACTIONr_mcangle_it2.2432.8264490
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 361 -
Rwork0.241 6727 -
all-7088 -
obs--99.42 %
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)
11.54010.61781.00530.6196-0.10531.4613-0.24910.02190.3005-0.1050.11230.1671-0.3425-0.10340.13670.3254-0.0212-0.01020.1062-0.06150.17081.98835.477137.0682
20.74140.22760.02330.54720.21050.88420.0491-0.05930.05170.0077-0.00730.0587-0.0652-0.036-0.04180.0619-0.0227-0.0060.0534-0.00810.0226-4.00975.996921.0715
31.71761.15371.16311.69571.40992.01320.0946-0.013-0.13560.22160.0912-0.24960.20510.0973-0.18580.12450.0188-0.0190.086-0.05710.064511.405723.205250.8271
44.5398-0.1634-0.28443.52261.18452.76420.2840.11470.4533-0.2104-0.51950.6612-0.2078-0.72670.23550.0550.07610.01780.253-0.09780.2305-27.649513.876631.6873
50.71360.00580.02490.6494-0.00310.88880.0689-0.02610.054-0.036-0.0434-0.0319-0.04850.1281-0.02550.0612-0.0371-0.00640.0949-0.01640.034816.77116.085211.4357
60.64540.0168-0.27650.88760.290.64710.129-0.1620.1516-0.06330.014-0.1293-0.19820.2399-0.1430.1133-0.11260.04190.1305-0.0550.069325.434719.90818.3179
72.2928-0.724-0.60442.1466-0.87723.5137-0.224-0.1442-0.56190.1409-0.02830.29580.5122-0.19160.25240.1242-0.0330.09590.04310.01730.159217.075-20.297117.5394
81.44871.4281-1.23182.8323-1.19891.67910.0022-0.2301-0.1163-0.1103-0.0442-0.4614-0.08970.24960.0420.0456-0.05660.03280.1126-0.02840.098840.76419.27376.421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A243 - 284
2X-RAY DIFFRACTION2A285 - 518
3X-RAY DIFFRACTION3A519 - 652
4X-RAY DIFFRACTION4A653 - 746
5X-RAY DIFFRACTION5B251 - 364
6X-RAY DIFFRACTION6B365 - 536
7X-RAY DIFFRACTION7B537 - 623
8X-RAY DIFFRACTION8B624 - 746

+
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://pdbjlvh1.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