[English] 日本語
Yorodumi
- PDB-7sak: Crystal Structure of LaM4 Nanobody bound to mCherry -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sak
TitleCrystal Structure of LaM4 Nanobody bound to mCherry
Components
  • LaM4
  • mCherry
KeywordsIMMUNE SYSTEM / Antibody / nanobody / affinity tag / fluorescent protein
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesDiscosoma sp. (sea anemone)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsCong, A.T.Q. / Schellenberg, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Protein Sci. / Year: 2022
Title: High-efficiency recombinant protein purification using mCherry and YFP nanobody affinity matrices.
Authors: Cong, A.T.Q. / Witter, T.L. / Schellenberg, M.J.
History
DepositionSep 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: mCherry
B: LaM4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6494
Polymers42,5082
Non-polymers1422
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-17 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.554, 41.920, 47.827
Angle α, β, γ (deg.)90.000, 94.370, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-252-

HOH

21B-291-

HOH

-
Components

#1: Protein mCherry


Mass: 26996.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
#2: Antibody LaM4


Mass: 15511.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 1.84 Å3/Da / Density % sol: 33.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20 % PEG3350, 100 mM MMT (Malic Acid, MES and TRIS)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2020
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.15→75 Å / Num. obs: 207109 / % possible obs: 97 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.027 / Rrim(I) all: 0.086 / Χ2: 1.016 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.15-1.195.90.41784750.910.1810.4560.87677.3
1.19-1.247.90.355102410.9480.1320.3790.92793.9
1.24-1.39.90.294109040.9730.0970.311.02499.4
1.3-1.3610.20.239108870.9780.0770.2511.02699.6
1.36-1.459.60.186109990.9850.0630.1961.05999.9
1.45-1.5610.20.14109380.9920.0460.1481.044100
1.56-1.7210.50.109110120.9940.0350.1141.033100
1.72-1.979.80.085109790.9950.0290.091.038100
1.97-2.4810.40.072110820.9960.0230.0761.017100
2.48-7510.30.061112580.9980.020.0641.00999.9

-
Processing

Software
NameVersionClassification
PHENIX1.17refinement
DENZO720data reduction
SCALEPACK720data scaling
PHASER1.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H5Q

2h5q


Resolution: 1.15→42.15 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 13.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1439 10288 4.97 %
Rwork0.1173 196620 -
obs0.1186 206908 95.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.6 Å2 / Biso mean: 16.0711 Å2 / Biso min: 2.6 Å2
Refinement stepCycle: final / Resolution: 1.15→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 15 481 3221
Biso mean--20.9 32.94 -
Num. residues----345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.160.2391900.21063583377352
1.16-1.170.19372660.19025044531073
1.17-1.190.23162480.17335587583581
1.19-1.20.16953450.16125936628187
1.2-1.220.15513020.14356457675993
1.22-1.240.14923410.1376533687495
1.24-1.250.15653460.13686696704298
1.25-1.270.18163610.1366771713297
1.27-1.290.16673220.13396783710599
1.29-1.310.17383270.12646690701798
1.31-1.340.16644040.12096778718299
1.34-1.360.14323650.11446829719498
1.36-1.390.15613420.10696844718699
1.39-1.410.13173470.1046758710599
1.41-1.450.14183850.10456817720299
1.45-1.480.13873640.100167907154100
1.48-1.520.13393470.09986816716399
1.52-1.560.12753510.10196852720399
1.56-1.60.12933590.09886791715099
1.6-1.650.14163540.10776855720999
1.65-1.710.1483670.10676801716899
1.71-1.780.13663670.10246831719899
1.78-1.860.12833670.09976854722199
1.86-1.960.13263430.09996781712499
1.96-2.080.11963620.102569027264100
2.08-2.250.12923440.107568637207100
2.25-2.470.12963810.112968197200100
2.47-2.830.14413580.118768577215100
2.83-3.560.14433650.122168527217100
3.56-42.150.15463680.133668507218100

+
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