[English] 日本語
Yorodumi
- PDB-5u64: Camel nanobody VHH-28 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u64
TitleCamel nanobody VHH-28
ComponentsVHH-28
KeywordsIMMUNE SYSTEM / neutralizing antibody / camel vhh nanobody / HIV-1
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.153 Å
AuthorsStanfield, R.L. / Wilson, I.A.
CitationJournal: Sci Rep / Year: 2017
Title: Selection of nanobodies with broad neutralizing potential against primary HIV-1 strains using soluble subtype C gp140 envelope trimers.
Authors: Koch, K. / Kalusche, S. / Torres, J.L. / Stanfield, R.L. / Danquah, W. / Khazanehdari, K. / von Briesen, H. / Geertsma, E.R. / Wilson, I.A. / Wernery, U. / Koch-Nolte, F. / Ward, A.B. / Dietrich, U.
History
DepositionDec 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: VHH-28


Theoretical massNumber of molelcules
Total (without water)15,0201
Polymers15,0201
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.790, 76.937, 69.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-341-

HOH

21B-361-

HOH

-
Components

#1: Antibody VHH-28


Mass: 15020.442 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1M sodium citrate, 0.1M CHES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.15→28.4 Å / Num. obs: 53677 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.88 / Rmerge(I) obs: 0.098 / Net I/σ(I): 17.2
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.45 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.153→28.395 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.01
RfactorNum. reflection% reflection
Rfree0.1703 2706 5.05 %
Rwork0.1454 --
obs0.1467 53637 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.153→28.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 0 167 1145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0221176
X-RAY DIFFRACTIONf_angle_d1.7581630
X-RAY DIFFRACTIONf_dihedral_angle_d19.05466
X-RAY DIFFRACTIONf_chiral_restr0.125172
X-RAY DIFFRACTIONf_plane_restr0.012215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1531-1.1740.32711250.32062546X-RAY DIFFRACTION95
1.174-1.19660.28931380.272672X-RAY DIFFRACTION99
1.1966-1.2210.22121530.2232625X-RAY DIFFRACTION100
1.221-1.24760.2021410.20572656X-RAY DIFFRACTION100
1.2476-1.27660.22341350.18612652X-RAY DIFFRACTION100
1.2766-1.30850.19881360.18232670X-RAY DIFFRACTION99
1.3085-1.34390.18241360.15752684X-RAY DIFFRACTION100
1.3439-1.38350.18371370.14252681X-RAY DIFFRACTION100
1.3835-1.42810.17021670.14142648X-RAY DIFFRACTION100
1.4281-1.47920.14071480.13092671X-RAY DIFFRACTION100
1.4792-1.53840.13191390.12392678X-RAY DIFFRACTION99
1.5384-1.60840.15011550.10542652X-RAY DIFFRACTION100
1.6084-1.69320.14241480.10862697X-RAY DIFFRACTION100
1.6932-1.79920.12881350.11652689X-RAY DIFFRACTION100
1.7992-1.93810.1291500.11632678X-RAY DIFFRACTION99
1.9381-2.13310.15281460.11562694X-RAY DIFFRACTION100
2.1331-2.44160.16361310.12912748X-RAY DIFFRACTION100
2.4416-3.07560.18441490.15272734X-RAY DIFFRACTION99
3.0756-28.40360.18051370.15842856X-RAY DIFFRACTION99

+
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