[English] 日本語
Yorodumi
- PDB-7yn3: Crystal structure of CcbD complex with CcbZ carrier protein domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yn3
TitleCrystal structure of CcbD complex with CcbZ carrier protein domain
Components
  • CcbD
  • CcbZ
KeywordsLYASE / lincomycin / celesticetin / amide bond forming enzyme
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / : / GFO/IDH/MocA C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
1,1'-ethane-1,2-diyldipyrrolidine-2,5-dione / 4'-PHOSPHOPANTETHEINE / CcbZ / CcbD
Similarity search - Component
Biological speciesStreptomyces caelestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMori, T. / Lyu, S. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of CcbD complex with carrier protein
Authors: Mori, T. / Lyu, S. / Abe, I.
History
DepositionJul 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CcbD
B: CcbD
C: CcbZ
D: CcbZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7918
Polymers98,6264
Non-polymers1,1654
Water11,295627
1
A: CcbD
C: CcbZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8954
Polymers49,3132
Non-polymers5832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CcbD
D: CcbZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8954
Polymers49,3132
Non-polymers5832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.572, 90.104, 124.411
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 CcbD


Mass: 40806.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces caelestis (bacteria) / Gene: HDA41_002772 / Production host: Escherichia coli (E. coli) / References: UniProt: E9JES9
#2: Protein CcbZ / Putative dehydrogenase/acyl carrier protein


Mass: 8506.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces caelestis (bacteria) / Gene: HDA41_002769 / Production host: Escherichia coli (E. coli) / References: UniProt: E9JES6
#3: Chemical ChemComp-1N2 / 1,1'-ethane-1,2-diyldipyrrolidine-2,5-dione


Mass: 224.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES (pH 6.7), 0.16 M magnesium chloride, 0.2 M sodium thiocyanate, 8% w/v PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.07 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.1→44.79 Å / Num. obs: 59483 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 27.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.7
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4565 / CC1/2: 0.848 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YN1

7yn1


Resolution: 2.1→44.79 Å / SU ML: 0.2202 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.6361
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2264 1994 3.36 %
Rwork0.1754 57412 -
obs0.177 59406 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.56 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6525 0 74 627 7226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00666779
X-RAY DIFFRACTIONf_angle_d0.8559251
X-RAY DIFFRACTIONf_chiral_restr0.04651034
X-RAY DIFFRACTIONf_plane_restr0.00881220
X-RAY DIFFRACTIONf_dihedral_angle_d15.64272503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.25961400.21854050X-RAY DIFFRACTION99.98
2.15-2.210.30721390.20694032X-RAY DIFFRACTION99.98
2.21-2.280.24891410.19114045X-RAY DIFFRACTION99.93
2.28-2.350.25191450.18894055X-RAY DIFFRACTION100
2.35-2.430.24341400.19124090X-RAY DIFFRACTION99.95
2.43-2.530.25451430.18874026X-RAY DIFFRACTION100
2.53-2.650.2711430.19874102X-RAY DIFFRACTION99.95
2.65-2.790.2441410.20014054X-RAY DIFFRACTION99.98
2.79-2.960.27131420.19834102X-RAY DIFFRACTION99.91
2.96-3.190.23131370.18374099X-RAY DIFFRACTION99.93
3.19-3.510.22691430.18144089X-RAY DIFFRACTION99.98
3.51-4.020.18911440.15584145X-RAY DIFFRACTION100
4.02-5.060.2041440.1434182X-RAY DIFFRACTION100
5.06-44.790.18561520.15634341X-RAY DIFFRACTION99.73

+
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