[English] 日本語
Yorodumi
- PDB-9yru: Crystal structure of Apo Cysteinyl-tRNA synthetase (CysRS) from P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9yru
TitleCrystal structure of Apo Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Orthrhombic P form)
ComponentsCysteine--tRNA ligase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Cysteinyl-tRNA synthetase / CysRS
Function / homology
Function and homology information


cysteine-tRNA ligase / cysteine-tRNA ligase activity / cysteinyl-tRNA aminoacylation / apicoplast / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Cysteine-tRNA ligase / Cysteinyl-tRNA synthetase/mycothiol ligase / tRNA synthetases class I, catalytic domain / tRNA synthetases class I (C) catalytic domain / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
cysteine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Apo Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Orthrhombic P form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionOct 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,1974
Polymers109,0662
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-80 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.874, 104.024, 158.805
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cysteine--tRNA ligase / Cysteinyl-tRNA synthetase


Mass: 54533.195 Da / Num. of mol.: 2 / Fragment: residues 91-535
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1015200.1 / Plasmid: PlfaA.00133.a.A3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IJP3, cysteine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: Berkeley D7: 100mM potassium phosphate dibasic, 100 mM potassium chloride, 30% PEG 3350. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 4mM ATP added to the protein prior to screening but ligand is ...Details: Berkeley D7: 100mM potassium phosphate dibasic, 100 mM potassium chloride, 30% PEG 3350. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 4mM ATP added to the protein prior to screening but ligand is not bound likely due to high phosphate concentration in the crystallant. plate 20147 D7 drop 1 , Puck: PSL-0309, Cryo: direct

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 26, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.06→49.77 Å / Num. obs: 20666 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.031 / Rrim(I) all: 0.114 / Χ2: 1.21 / Net I/σ(I): 16.7 / Num. measured all: 270129
Reflection shellResolution: 3.06→3.14 Å / % possible obs: 99.9 % / Redundancy: 13.4 % / Rmerge(I) obs: 2.163 / Num. measured all: 19643 / Num. unique obs: 1464 / CC1/2: 0.767 / Rpim(I) all: 0.611 / Rrim(I) all: 2.249 / Χ2: 1 / Net I/σ(I) obs: 1.4

-
Processing

Software
NameVersionClassification
PHENIX(2.0_5765: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→49.77 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 1041 5.06 %
Rwork0.2285 --
obs0.2315 20574 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.06→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6521 0 2 0 6523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046696
X-RAY DIFFRACTIONf_angle_d0.7919105
X-RAY DIFFRACTIONf_dihedral_angle_d13.5232270
X-RAY DIFFRACTIONf_chiral_restr0.0521010
X-RAY DIFFRACTIONf_plane_restr0.0061160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.220.55671320.41772724X-RAY DIFFRACTION100
3.22-3.420.37591530.31552723X-RAY DIFFRACTION99
3.42-3.690.35621670.29322738X-RAY DIFFRACTION100
3.69-4.060.27171370.20972770X-RAY DIFFRACTION100
4.06-4.640.25061490.18452793X-RAY DIFFRACTION100
4.65-5.850.25751390.20342843X-RAY DIFFRACTION100
5.85-49.770.26721640.22152942X-RAY DIFFRACTION100
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)
10.2663-0.2726-0.35290.468-0.03970.82790.0527-0.0529-0.29690.28170.0865-0.03740.4632-0.2713-00.8218-0.07310.05250.8536-0.02460.985325.096933.281523.9541
20.14440.0199-0.0035-0.01450.0015-0.0162-0.5608-0.07290.4726-0.31770.1636-0.3982-0.53250.0129-00.69540.0467-0.10750.8846-0.01710.88899.446937.104621.5754
31.67990.23420.66230.62510.25620.2994-0.10890.03440.0204-0.02540.1566-0.283-0.9601-1.134400.9891-0.0682-0.02831.2436-0.03111.02657.552741.072320.6599
40.25390.19340.24620.24230.27920.624-0.39110.7251-0.0788-0.61270.3939-0.0767-0.76810.139701.5434-0.26220.14641.2686-0.0731.090515.579332.7973-2.4407
50.1336-0.1826-0.09540.2860.14920.07330.45340.62720.39640.1414-0.06760.0451-0.0008-0.1507-01.34510.063-0.15561.37340.0750.89045.32642.17257.0949
60.2298-0.0224-0.05580.0280.04040.05850.0315-0.2248-0.2656-0.6875-0.17120.35690.28010.011401.4399-0.1914-0.01310.97170.02190.906820.606135.015312.3471
70.7635-0.02870.5250.77820.39290.87970.1780.091-0.4054-0.6012-0.0085-0.30450.69530.5743-0.00091.2702-0.3218-0.07170.85140.04860.991114.80723.222927.5702
80.5825-0.0477-0.21860.0764-0.00110.08590.0159-0.7305-0.68710.34060.01880.29450.1564-0.454201.3389-0.3257-0.00841.28940.24091.283518.132422.706152.1622
91.01380.52020.43590.28340.27030.37480.3476-0.4046-0.44510.80260.17840.20870.7346-0.3835-01.22330.1208-0.24650.93770.0350.954230.846826.361250.9012
100.86580.76760.23211.5784-0.75571.04310.2843-0.4468-0.25040.4850.0978-0.20120.39870.090301.0245-0.0192-0.20091.0313-0.09220.985142.396642.527359.9398
110.3095-0.06670.05540.6778-0.32520.9530.41980.0060.38020.4451-0.3345-0.4301-0.35260.13090.05480.7689-0.1017-0.33221.1457-0.12091.327654.362245.122664.0536
121.0242-0.39210.12970.75210.9961.8096-0.06040.07780.2046-0.1853-0.040.0564-0.6447-0.2008-00.96110.00620.00490.89720.03351.010322.948355.121743.2738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 113 )
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 159 )
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 225 )
5X-RAY DIFFRACTION5chain 'A' and (resid 226 through 255 )
6X-RAY DIFFRACTION6chain 'A' and (resid 256 through 285 )
7X-RAY DIFFRACTION7chain 'A' and (resid 286 through 348 )
8X-RAY DIFFRACTION8chain 'A' and (resid 349 through 374 )
9X-RAY DIFFRACTION9chain 'A' and (resid 375 through 458 )
10X-RAY DIFFRACTION10chain 'B' and (resid 16 through 159 )
11X-RAY DIFFRACTION11chain 'B' and (resid 160 through 316 )
12X-RAY DIFFRACTION12chain 'B' and (resid 317 through 458 )

+
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