[English] 日本語
Yorodumi
- PDB-8ynq: ATP-grasp peptide ligase from Streptomyces -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ynq
TitleATP-grasp peptide ligase from Streptomyces
ComponentsATP-grasp peptide ligase
KeywordsLIGASE / ATP-grasp enzymes / peptide ligase / Amide synthase
Function / homologyADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesStreptomyces albogriseolus 1-36 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsXu, M.J. / Yan, Y.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2025
Title: Structural Insights into the Substrate Recognition Mechanism of an ATP-Grasp Peptide-Ligase Producing Diverse Dipeptides Containing Unnatural Amino Acids
Authors: Yan, Y.Q. / Li, S.Y. / Wu, X.N. / Zhou, T. / Li, J.X. / Huang, S.X. / Zheng, J.T. / Xu, J. / Da, L.T. / Xu, M.J.
History
DepositionMar 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: ATP-grasp peptide ligase
D: ATP-grasp peptide ligase
A: ATP-grasp peptide ligase
B: ATP-grasp peptide ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,19124
Polymers196,7754
Non-polymers3,41720
Water5,855325
1
C: ATP-grasp peptide ligase
D: ATP-grasp peptide ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,43412
Polymers98,3872
Non-polymers2,04610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-9 kcal/mol
Surface area33220 Å2
MethodPISA
2
A: ATP-grasp peptide ligase
B: ATP-grasp peptide ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,75812
Polymers98,3872
Non-polymers1,37010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint12 kcal/mol
Surface area33260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.856, 97.518, 101.514
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules CDAB

#1: Protein
ATP-grasp peptide ligase


Mass: 49193.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SRA: SRR28004724
Source: (gene. exp.) Streptomyces albogriseolus 1-36 (bacteria)
Gene: Alb28 / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 7 types, 345 molecules

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


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: MgCl2.6H2O, Tris, PEG smear High, Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: STFC Large Pixel Detector / Detector: PIXEL / Date: Nov 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 68197 / % possible obs: 99.6 % / Redundancy: 3.2 % / CC1/2: 0.941 / CC star: 0.985 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.1 / Rrim(I) all: 0.184 / Χ2: 0.819 / Net I/σ(I): 6.4 / Num. measured all: 219848
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.45-2.492.70.49533160.7930.940.3360.60.68497.8
2.49-2.542.90.45933850.8130.9470.3030.5520.64699.2
2.54-2.5930.4533870.8560.960.2930.5390.67199.4
2.59-2.643.10.44633540.830.9520.2890.5340.68199.3
2.64-2.73.10.41133980.830.9530.2680.4920.70399.7
2.7-2.763.10.34633920.90.9730.2290.4170.73999.9
2.76-2.833.30.31734260.910.9760.2030.3780.75799.8
2.83-2.93.20.30333870.8870.970.1980.3630.80399.7
2.9-2.993.40.2734230.9180.9780.1720.3210.81699.9
2.99-3.093.40.24534100.910.9760.1550.2910.84699.9
3.09-3.23.40.22234090.9250.980.1410.2640.96199.7
3.2-3.323.30.19633850.9270.9810.1270.2350.99899.9
3.32-3.483.30.17934210.9260.9810.1160.2141.023100
3.48-3.663.20.16734060.9270.9810.110.21.09199.8
3.66-3.893.40.1534390.9520.9880.0950.1781.00199.9
3.89-4.193.40.14133890.9440.9860.090.1680.97199.9
4.19-4.613.30.13434610.9560.9890.0860.1590.999.8
4.61-5.283.30.12334300.9560.9890.0790.1460.777100
5.28-6.653.30.11334550.9520.9880.0730.1350.6599.9
6.65-503.20.09135240.970.9920.060.1090.53999.4

-
Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.19.2-4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.45→47.93 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 37.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3188 2728 4.77 %
Rwork0.2337 --
obs0.2378 57209 83.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12595 0 219 325 13139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913065
X-RAY DIFFRACTIONf_angle_d1.13817735
X-RAY DIFFRACTIONf_dihedral_angle_d11.9831862
X-RAY DIFFRACTIONf_chiral_restr0.0561975
X-RAY DIFFRACTIONf_plane_restr0.012308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.490.4904770.3321018X-RAY DIFFRACTION30
2.49-2.540.451700.29671446X-RAY DIFFRACTION43
2.54-2.590.3362630.27951641X-RAY DIFFRACTION48
2.59-2.650.35321090.29511957X-RAY DIFFRACTION57
2.65-2.710.3786890.31142268X-RAY DIFFRACTION66
2.71-2.780.4531110.31082668X-RAY DIFFRACTION77
2.78-2.860.38271450.30773008X-RAY DIFFRACTION88
2.86-2.940.39581430.30853205X-RAY DIFFRACTION93
2.94-3.030.39781270.27313420X-RAY DIFFRACTION98
3.03-3.140.39992000.26853336X-RAY DIFFRACTION98
3.14-3.270.32651630.25983418X-RAY DIFFRACTION98
3.27-3.420.33182120.24063325X-RAY DIFFRACTION98
3.42-3.60.33242010.23223357X-RAY DIFFRACTION98
3.6-3.820.31491850.21653340X-RAY DIFFRACTION98
3.82-4.120.27641840.19663385X-RAY DIFFRACTION98
4.12-4.530.25122270.19153344X-RAY DIFFRACTION98
4.53-5.190.28661960.20033387X-RAY DIFFRACTION98
5.19-6.530.29911490.23033475X-RAY DIFFRACTION99
6.53-47.930.2666770.19743483X-RAY DIFFRACTION95

+
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