[English] 日本語
Yorodumi
- PDB-8zil: Gamma-lyase CndF in complex with ethyl acetoacetate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zil
TitleGamma-lyase CndF in complex with ethyl acetoacetate
ComponentsPLP dependent gamma-lyase CndF
KeywordsLYASE / PLP dependent / Gamma-lyase / C-C bond formation
Function / homologyethyl 3-oxobutanoate / PHOSPHATE ION
Function and homology information
Biological speciesPenicillium citrinum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGao, Y. / Zhou, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2025
Title: Structure and Mechanism of the Pyridoxal 5'-Phosphate-Dependent Amino Acid gamma-Substitution Enzyme in 6-Alkyl-Pipecolate Biosynthesis
Authors: Gao, Y. / Wang, B. / Zhou, J. / Gu, Y.
History
DepositionMay 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 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.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
A: PLP dependent gamma-lyase CndF
B: PLP dependent gamma-lyase CndF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4195
Polymers126,0992
Non-polymers3203
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-42 kcal/mol
Surface area37080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.842, 101.768, 127.985
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein PLP dependent gamma-lyase CndF


Mass: 63049.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence matches GenBank Code KAK5801372.1, except for two mismatches (F15L and L561F).
Source: (gene. exp.) Penicillium citrinum (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EAC / ethyl 3-oxobutanoate


Mass: 130.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M sodium sulfate, 0.1M Bis-Tris propane pH 7.5, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.65→45.81 Å / Num. obs: 33298 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.68 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.079 / Net I/σ(I): 13
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 2 / Num. unique obs: 4372 / CC1/2: 0.7 / Rpim(I) all: 0.586 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→45.81 Å / SU ML: 0.3522 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2663 1591 4.8 %
Rwork0.2477 31576 -
obs0.2486 33167 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.73 Å2
Refinement stepCycle: LAST / Resolution: 2.65→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7335 0 19 98 7452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00457520
X-RAY DIFFRACTIONf_angle_d0.76810224
X-RAY DIFFRACTIONf_chiral_restr0.05041149
X-RAY DIFFRACTIONf_plane_restr0.00531323
X-RAY DIFFRACTIONf_dihedral_angle_d15.50622721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.740.37861360.36262846X-RAY DIFFRACTION99.7
2.74-2.830.37561530.34152810X-RAY DIFFRACTION99.73
2.83-2.950.29621380.30072834X-RAY DIFFRACTION100
2.95-3.080.31271480.28572869X-RAY DIFFRACTION100
3.08-3.240.28951520.28222812X-RAY DIFFRACTION100
3.24-3.450.27921440.2652848X-RAY DIFFRACTION100
3.45-3.710.27371590.24892843X-RAY DIFFRACTION99.4
3.71-4.090.30541360.23772867X-RAY DIFFRACTION99.44
4.09-4.680.25451290.21762863X-RAY DIFFRACTION98.81
4.68-5.890.21851510.21912921X-RAY DIFFRACTION99.97
5.89-45.810.19551450.2093063X-RAY DIFFRACTION99.69

+
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