[English] 日本語
Yorodumi
- PDB-8ein: Crystal structure of WT cyanophycin dipeptide hydrolase CphZ from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ein
TitleCrystal structure of WT cyanophycin dipeptide hydrolase CphZ from Acinetobacter baylyi DSM587
ComponentsSuccinylglutamate desuccinylase
KeywordsHYDROLASE / CphZ / cyanophycin
Function / homology: / Succinylglutamate desuccinylase/aspartoacylase / Succinylglutamate desuccinylase / Aspartoacylase family / hydrolase activity, acting on ester bonds / metal ion binding / : / Succinylglutamate desuccinylase/aspartoacylase
Function and homology information
Biological speciesAcinetobacter baylyi ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSharon, I. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Discovery of cyanophycin dipeptide hydrolase enzymes suggests widespread utility of the natural biopolymer cyanophycin.
Authors: Sharon, I. / McKay, G.A. / Nguyen, D. / Schmeing, T.M.
History
DepositionSep 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Succinylglutamate desuccinylase
B: Succinylglutamate desuccinylase
C: Succinylglutamate desuccinylase
D: Succinylglutamate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,38412
Polymers164,9034
Non-polymers4818
Water00
1
A: Succinylglutamate desuccinylase
B: Succinylglutamate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6926
Polymers82,4512
Non-polymers2414
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-115 kcal/mol
Surface area29520 Å2
MethodPISA
2
C: Succinylglutamate desuccinylase
D: Succinylglutamate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6926
Polymers82,4512
Non-polymers2414
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-115 kcal/mol
Surface area29070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.632, 128.015, 107.078
Angle α, β, γ (deg.)90.00, 129.48, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Succinylglutamate desuccinylase


Mass: 41225.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baylyi ADP1 (bacteria) / Strain: ATCC 33305 / BD413 / ADP1 / Gene: ACIAD1282 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6FCQ4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M bis-tris propane pH 7.5, 24% PEG3350, 0.2 M NaBr, 10 mM spermine and 10 mM LiCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→81.8 Å / Num. obs: 39871 / % possible obs: 83.81 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.037 / Net I/σ(I): 15.26
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 1138 / CC1/2: 0.847

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ab initio model generated with Rosetta

Resolution: 2.7→48.94 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 33.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2622 1980 4.97 %RANDOM
Rwork0.2422 ---
obs0.2433 39871 91.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11440 0 8 0 11448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014
X-RAY DIFFRACTIONf_angle_d1.772
X-RAY DIFFRACTIONf_dihedral_angle_d12.5144367
X-RAY DIFFRACTIONf_chiral_restr0.0881770
X-RAY DIFFRACTIONf_plane_restr0.0072130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.4431440.40082219X-RAY DIFFRACTION76
2.77-2.840.38921460.35522848X-RAY DIFFRACTION97
2.84-2.930.3581460.32462847X-RAY DIFFRACTION96
2.93-3.020.3311360.30992789X-RAY DIFFRACTION95
3.02-3.130.33761460.32092894X-RAY DIFFRACTION98
3.13-3.250.3241350.3262921X-RAY DIFFRACTION98
3.25-3.40.36251330.32915X-RAY DIFFRACTION98
3.4-3.580.29071420.27582906X-RAY DIFFRACTION98
3.58-3.810.29241620.25212872X-RAY DIFFRACTION97
3.81-4.10.29721520.24442759X-RAY DIFFRACTION94
4.1-4.510.25691270.22512468X-RAY DIFFRACTION83
4.51-5.160.21761430.20182480X-RAY DIFFRACTION84
5.16-6.50.24271130.22052588X-RAY DIFFRACTION86
6.5-48.940.18171550.17522385X-RAY DIFFRACTION80

+
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