[English] 日本語
Yorodumi
- PDB-8cpl: YZw2 a scaffold for cryo-EM of small proteins of interest -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cpl
TitleYZw2 a scaffold for cryo-EM of small proteins of interest
ComponentsPutrescine aminotransferase,Immunoglobulin G-binding protein A
KeywordsSTRUCTURAL PROTEIN / Scaffold Fusion protein
Function / homology
Function and homology information


diamine transaminase / putrescine-2-oxoglutarate transaminase / diamine transaminase activity / putrescine--2-oxoglutarate transaminase activity / L-lysine catabolic process / putrescine catabolic process / IgG binding / pyridoxal phosphate binding / protein homodimerization activity / extracellular region ...diamine transaminase / putrescine-2-oxoglutarate transaminase / diamine transaminase activity / putrescine--2-oxoglutarate transaminase activity / L-lysine catabolic process / putrescine catabolic process / IgG binding / pyridoxal phosphate binding / protein homodimerization activity / extracellular region / identical protein binding / cytosol
Similarity search - Function
Putrescine aminotransferase / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / : / LysM domain / LysM domain profile. ...Putrescine aminotransferase / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / : / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / Aminotransferases class-III pyridoxal-phosphate attachment site. / YSIRK type signal peptide / Aminotransferase class-III / Aminotransferase class-III / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Immunoglobulin G-binding protein A / Putrescine aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.605 Å
AuthorsMoche, M. / Friberg, O. / Nygren, P.A. / Nilvebrant, J.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Clas Groschinsky Memorial FundM19380 Sweden
Sven and Dagmar Salens Foundation Sweden
CitationJournal: To Be Published
Title: Engineered imaging scaffolds for cryo-EM of small proteins of interest.
Authors: Moche, M. / Nygren, P.A. / Nilvebrant, J.
History
DepositionMar 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putrescine aminotransferase,Immunoglobulin G-binding protein A
B: Putrescine aminotransferase,Immunoglobulin G-binding protein A
C: Putrescine aminotransferase,Immunoglobulin G-binding protein A
D: Putrescine aminotransferase,Immunoglobulin G-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,8588
Polymers217,8694
Non-polymers9894
Water39,5252194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30800 Å2
ΔGint-215 kcal/mol
Surface area57510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.453, 173.903, 209.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Putrescine aminotransferase,Immunoglobulin G-binding protein A / PAT / PATase / Cadaverine transaminase / Diamine transaminase / Putrescine transaminase / ...PAT / PATase / Cadaverine transaminase / Diamine transaminase / Putrescine transaminase / Putrescine--2-oxoglutaric acid transaminase / Putrescine:2-OG aminotransferase / IgG-binding protein A / Staphylococcal protein A / SpA


Mass: 54467.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Our protein YZw2 is a fusion protein connecting P42588 7-457 with P38507 278-327.,Our protein YZw2 is a fusion protein connecting P42588 7-457 with P38507 278-327.
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Staphylococcus aureus (bacteria)
Gene: patA, ygjG, b3073, JW5510, spa / Production host: Escherichia coli (E. coli)
References: UniProt: P42588, UniProt: P38507, putrescine-2-oxoglutarate transaminase, diamine transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2194 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 16.6% w/v PEG3350, 0.2M NaF and 0.1M Bis-Tris Propane pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.6→49.44 Å / Num. obs: 203302 / % possible obs: 58.4 % / Redundancy: 13.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.048 / Rrim(I) all: 0.178 / Net I/σ(I): 10
Reflection shellResolution: 1.605→1.751 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.719 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 10164 / CC1/2: 0.618 / Rpim(I) all: 0.485 / Rrim(I) all: 1.788 / % possible all: 12.8

-
Processing

Software
NameVersionClassification
BUSTER2.10.4 (26-JUL-2023)refinement
STARANISOdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.605→49.44 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.117
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 10086 4.96 %RANDOM
Rwork0.1877 ---
obs0.1888 203302 58.4 %-
Displacement parametersBiso mean: 22.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.9178 Å20 Å20 Å2
2---1.3356 Å20 Å2
3---0.4178 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.605→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14159 0 64 2194 16417
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115317HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0120843HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5452SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2712HARMONIC5
X-RAY DIFFRACTIONt_it15317HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion16.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1992SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16105SEMIHARMONIC4
LS refinement shellResolution: 1.605→1.69 Å
RfactorNum. reflection% reflection
Rfree0.3074 183 4.5 %
Rwork0.2976 3884 -
obs--8.12 %

+
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