[English] 日本語
Yorodumi
- PDB-4q24: Crystal structure of Cyclo(L-leucyl-L-phenylalanyl) synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q24
TitleCrystal structure of Cyclo(L-leucyl-L-phenylalanyl) synthase
ComponentsCyclo(L-leucyl-L-phenylalanyl) synthase
Keywordstransferase/transferase inhibitor / Rossmann fold / cyclodipeptide synthase / aminoacyl-tRNA / transferase-transferase inhibitor complex
Function / homology
Function and homology information


cyclo(L-leucyl-L-phenylalanyl) synthase / aminoacyltransferase activity / antibacterial peptide biosynthetic process
Similarity search - Function
Cyclodipeptide synthase / Cyclodipeptide synthase superfamily / Cyclodipeptide synthase / Cyclodipeptide synthase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-XVE / Cyclo(L-leucyl-L-phenylalanyl) synthase
Similarity search - Component
Biological speciesStreptomyces noursei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMoutiez, M. / Schmitt, E. / Seguin, J. / Thai, R. / Favry, E. / Mechulam, Y. / Gondry, M.
CitationJournal: Nat Commun / Year: 2014
Title: Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases.
Authors: Moutiez, M. / Schmitt, E. / Seguin, J. / Thai, R. / Favry, E. / Belin, P. / Mechulam, Y. / Gondry, M.
History
DepositionApr 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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: Cyclo(L-leucyl-L-phenylalanyl) synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2332
Polymers27,9011
Non-polymers3321
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.968, 86.968, 70.738
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Cyclo(L-leucyl-L-phenylalanyl) synthase / Cyclodipeptide synthase / CDPS


Mass: 27901.449 Da / Num. of mol.: 1 / Mutation: SC37
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces noursei (bacteria) / Gene: albC / Plasmid: PQE60 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8GED7, cyclo(L-leucyl-L-phenylalanyl) synthase
#2: Chemical ChemComp-XVE / PHENYLMETHYL N-[(2S)-4-CHLORO-3-OXO-1-PHENYL-BUTAN-2-YL]CARBAMATE


Mass: 331.793 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18ClNO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10%PEG8000, 50mM KCl, 50mM Na cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2012
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.9→37.7 Å / Num. all: 7023 / Num. obs: 7023 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.71 % / Biso Wilson estimate: 80.89 Å2 / Rsym value: 0.079 / Net I/σ(I): 11.45
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 2.72 % / Mean I/σ(I) obs: 1.75 / Num. unique all: 1109 / Rsym value: 0.606 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3OQV

3oqv


Resolution: 2.9→37.66 Å / Cor.coef. Fo:Fc: 0.9355 / Cor.coef. Fo:Fc free: 0.8853 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 350 5 %RANDOM
Rwork0.2007 ---
obs0.2034 7001 98.3 %-
all-7001 --
Displacement parametersBiso mean: 71.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.0403 Å20 Å20 Å2
2--0.0403 Å20 Å2
3----0.0807 Å2
Refine analyzeLuzzati coordinate error obs: 0.486 Å
Refinement stepCycle: LAST / Resolution: 2.9→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 22 3 1804
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091832HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.072468HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d673SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes278HARMONIC5
X-RAY DIFFRACTIONt_it1832HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion22.11
X-RAY DIFFRACTIONt_chiral_improper_torsion229SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2097SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2557 98 4.99 %
Rwork0.2302 1867 -
all0.2315 1965 -
obs--98.3 %
Refinement TLS params.Method: refined / Origin x: 33.8594 Å / Origin y: -8.3482 Å / Origin z: -2.9409 Å
111213212223313233
T0.0083 Å2-0.0673 Å2-0.0412 Å2--0.1504 Å2-0.0611 Å2---0.0932 Å2
L2.6181 °20.3377 °2-0.0724 °2-5.0501 °20.3477 °2--4.063 °2
S-0.0465 Å °0.1788 Å °-0.0116 Å °-0.115 Å °-0.1802 Å °0.1757 Å °0.1409 Å °-0.3093 Å °0.2267 Å °
Refinement TLS groupSelection details: { A|* }

+
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