[English] 日本語
Yorodumi
- PDB-8r2p: YZwIdeal x16 a scaffold for cryo-EM of small proteins of interest... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r2p
TitleYZwIdeal x16 a scaffold for cryo-EM of small proteins of interest crystallizing in space group 19 (P 21 21 21)
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. / Aminotransferase class-III / Aminotransferase class-III / YSIRK type signal peptide / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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
DepositionNov 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 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)229,2058
Polymers228,2164
Non-polymers9894
Water27,1491507
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30690 Å2
ΔGint-224 kcal/mol
Surface area57510 Å2
Unit cell
Length a, b, c (Å)73.260, 196.760, 208.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

-
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: 57054.121 Da / Num. of mol.: 4 / Mutation: G487A
Source method: isolated from a genetically manipulated source
Details: The polypeptide chain consists of P42588_7-457 and P38507_160-269 connected by a linker. P38507 is mutated at Gly240Ala corresponding to residue 487 in the model.,The polypeptide chain ...Details: The polypeptide chain consists of P42588_7-457 and P38507_160-269 connected by a linker. P38507 is mutated at Gly240Ala corresponding to residue 487 in the model.,The polypeptide chain consists of P42588_7-457 and P38507_160-269 connected by a linker. P38507 is mutated at Gly240Ala corresponding to residue 487 in the model.
Source: (gene. exp.) Escherichia coli (E. coli) / 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.: 1507 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50% w/v PEG200, 0.2M MgCl2 and 0.1M Sodium Cacodylate buffer pH 6.5
PH range: 6.5-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976246 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976246 Å / Relative weight: 1
ReflectionResolution: 2.217→48.91 Å / Num. obs: 61481 / % possible obs: 41.1 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.07 / Rrim(I) all: 0.182 / Net I/σ(I): 8.1
Reflection shellResolution: 2.217→2.425 Å / Redundancy: 5.12 % / Rmerge(I) obs: 1.041 / Mean I/σ(I) obs: 1.68 / Num. unique obs: 3073 / CC1/2: 0.665 / Rpim(I) all: 0.49 / Rrim(I) all: 1.156 / % possible all: 8.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
STARANISOdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→48.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.127 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23039 2928 4.8 %RANDOM
Rwork0.18628 ---
obs0.18846 58551 41.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.657 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.84 Å2-0 Å2
3----0.64 Å2
Refinement stepCycle: 1 / Resolution: 2.22→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14315 0 64 1507 15886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01315059
X-RAY DIFFRACTIONr_bond_other_d0.0010.01514576
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.6420441
X-RAY DIFFRACTIONr_angle_other_deg1.2431.57433573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25151966
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53222.97734
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.749152588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1561586
X-RAY DIFFRACTIONr_chiral_restr0.060.21964
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023398
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6993.3037750
X-RAY DIFFRACTIONr_mcbond_other2.6953.3037749
X-RAY DIFFRACTIONr_mcangle_it4.2664.949754
X-RAY DIFFRACTIONr_mcangle_other4.2664.9419755
X-RAY DIFFRACTIONr_scbond_it3.1843.6567309
X-RAY DIFFRACTIONr_scbond_other3.1843.6577306
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2355.35110688
X-RAY DIFFRACTIONr_long_range_B_refined9.63663.21566868
X-RAY DIFFRACTIONr_long_range_B_other9.38863.27965109
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A149200.05
12B149200.05
21A150000.05
22C150000.05
31A149400.06
32D149400.06
41B150380.06
42C150380.06
51B152290.06
52D152290.06
61C151850.07
62D151850.07
LS refinement shellResolution: 2.22→2.275 Å
RfactorNum. reflection% reflection
Rfree0.178 5 -
Rwork0.358 210 -
obs--1.96 %

+
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