[English] 日本語
Yorodumi
- PDB-5znj: Crystal structure of a bacterial ProRS with ligands -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5znj
TitleCrystal structure of a bacterial ProRS with ligands
ComponentsProline--tRNA ligase
KeywordsLIGASE / Aminoacyl-tRNA synthetase / Protein biosynthesis / Inhibitor
Function / homology
Function and homology information


YbaK protein / YbaK/aminoacyl-tRNA synthetase-associated domain / Anticodon-binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-HFG / PHOSPHATE ION / :
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsCheng, B. / Yu, Y. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81773636 China
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Guided Design of Halofuginone Derivatives as ATP-Aided Inhibitors Against Bacterial Prolyl-tRNA Synthetase.
Authors: Cheng, B. / Cai, Z. / Luo, Z. / Luo, S. / Luo, Z. / Cheng, Y. / Yu, Y. / Guo, J. / Ju, Y. / Gu, Q. / Xu, J. / Jiang, X. / Li, G. / Zhou, H.
History
DepositionApr 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Nov 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0706
Polymers63,9381
Non-polymers1,1325
Water4,918273
1
A: Proline--tRNA ligase
hetero molecules

A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,14012
Polymers127,8762
Non-polymers2,26410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7970 Å2
ΔGint-61 kcal/mol
Surface area45780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.139, 77.535, 74.226
Angle α, β, γ (deg.)90.00, 99.36, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 63937.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA (R3708) / Gene: proS, CT123_02285 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A227M497, proline-tRNA ligase

-
Non-polymers , 6 types, 278 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-HFG / 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one / Halofuginone


Mass: 414.681 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17BrClN3O3 / Comment: alkaloid, medication*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsThe authors did not cloned this gene from the standard strain of Staphylococcus aureus, but from a ...The authors did not cloned this gene from the standard strain of Staphylococcus aureus, but from a clinically drug-resistant strain (MRSA R3708). The author confirmed ProRS of MRSA R3708 shows THR 230, ALA 278.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 32 - 40% (v/v) Pentaerythritol propoxylate (5/4 PO/OH), 0.1 - 0.2 M KCl and 50 mM HEPES, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 62796 / % possible obs: 98.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 34.6
Reflection shellResolution: 1.84→1.91 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6339 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J3L

2j3l


Resolution: 1.84→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.455 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22249 3053 4.9 %RANDOM
Rwork0.19728 ---
obs0.19852 59229 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.912 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20.72 Å2
2--1.62 Å20 Å2
3----0.77 Å2
Refinement stepCycle: 1 / Resolution: 1.84→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 67 273 4724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194625
X-RAY DIFFRACTIONr_bond_other_d0.0020.024311
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9736288
X-RAY DIFFRACTIONr_angle_other_deg0.85439915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8865584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59824.612219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07715776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4291528
X-RAY DIFFRACTIONr_chiral_restr0.0640.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025318
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021058
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7953.272297
X-RAY DIFFRACTIONr_mcbond_other0.7953.272296
X-RAY DIFFRACTIONr_mcangle_it1.394.8982882
X-RAY DIFFRACTIONr_mcangle_other1.394.8982883
X-RAY DIFFRACTIONr_scbond_it0.743.2992328
X-RAY DIFFRACTIONr_scbond_other0.743.2992328
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2974.9293403
X-RAY DIFFRACTIONr_long_range_B_refined4.40725.7345225
X-RAY DIFFRACTIONr_long_range_B_other4.40725.7345225
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 238 -
Rwork0.28 4437 -
obs--99.85 %
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)
10.66750.431-0.17820.6806-0.18960.8620.00490.12820.061-0.0709-0.03960.1083-0.0484-0.14180.03460.09130.0054-0.0590.1448-0.01130.0611-18.2258-2.26320.4504
20.2811-0.0322-0.26460.1028-0.02760.55120.0006-0.0117-0.0424-0.0341-0.0107-0.018-0.0980.1030.010.0917-0.0281-0.01930.08960.00180.09745.03860.966632.8917
30.7598-0.2180.02991.0849-0.94330.87190.0161-0.07420.1091-0.1999-0.1368-0.13520.17120.1170.12070.1125-0.00950.03370.121-0.01590.094811.371-2.325212.2061
40.0175-0.0415-0.07231.1869-0.05450.7180.0390.0014-0.0082-0.2718-0.2683-0.4025-0.1262-0.12760.22930.13210.03690.05050.14620.04780.20115.747819.5513-2.9908
50.31940.62390.75351.85050.56843.1038-0.1223-0.134-0.0519-0.1875-0.3363-0.4826-0.6406-0.11320.45860.15290.0181-0.0490.1020.08630.242416.09125.60891.7722
60.30040.1596-0.64032.6579-0.51631.38180.0273-0.1818-0.1738-0.6036-0.4738-0.31550.04670.42170.44640.14130.09540.04490.18280.17950.305120.149915.1467-2.4541
70.36040.0534-0.16630.189-0.05490.1985-0.05550.0087-0.0811-0.1176-0.0104-0.03890.0487-0.01450.06590.1142-0.04540.00480.1117-0.01530.0806-9.5933-12.803123.3773
83.23962.1046-0.80833.1771-0.10721.387-0.21610.5412-0.6937-0.22610.1691-0.30290.1656-0.06220.0470.137-0.05280.04060.1357-0.15530.1878-17.1034-29.368315.9626
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 43
2X-RAY DIFFRACTION2A44 - 188
3X-RAY DIFFRACTION3A189 - 237
4X-RAY DIFFRACTION4A238 - 309
5X-RAY DIFFRACTION5A310 - 363
6X-RAY DIFFRACTION6A364 - 399
7X-RAY DIFFRACTION7A400 - 535
8X-RAY DIFFRACTION8A536 - 567

+
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