[English] 日本語
Yorodumi
- PDB-6xxo: Crystal structure of NB8, a nanobody targeting prostate specific ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xxo
TitleCrystal structure of NB8, a nanobody targeting prostate specific membrane antigen
ComponentsNB_8
KeywordsANTITUMOR PROTEIN / Nanobody / prostate-specific membrane antigen / antibody drug conjugate / cancer imaging / anti-cancer drugs.
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsShahar, A. / Rosenfeld, L. / Papo, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
European Research Council (ERC)336041 Israel
CitationJournal: J.Med.Chem. / Year: 2020
Title: Nanobodies Targeting Prostate-Specific Membrane Antigen for the Imaging and Therapy of Prostate Cancer.
Authors: Rosenfeld, L. / Sananes, A. / Zur, Y. / Cohen, S. / Dhara, K. / Gelkop, S. / Ben Zeev, E. / Shahar, A. / Lobel, L. / Akabayov, B. / Arbely, E. / Papo, N.
History
DepositionJan 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NB_8


Theoretical massNumber of molelcules
Total (without water)15,7141
Polymers15,7141
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.945, 68.857, 75.647
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-365-

HOH

-
Components

#1: Protein NB_8


Mass: 15714.057 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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M tri-Na Citrate pH 3.5, 3M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.5→28.52 Å / Num. obs: 23283 / % possible obs: 97.94 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0278 / Net I/σ(I): 28.37
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 3733 / CC1/2: 0.988 / Rrim(I) all: 0.117

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M7Q

5m7q


Resolution: 1.5→28.52 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.65
RfactorNum. reflection% reflection
Rfree0.1832 1107 4.76 %
Rwork0.1623 --
obs0.1634 23276 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→28.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 0 167 1130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071103
X-RAY DIFFRACTIONf_angle_d0.9431525
X-RAY DIFFRACTIONf_dihedral_angle_d2.7611040
X-RAY DIFFRACTIONf_chiral_restr0.06164
X-RAY DIFFRACTIONf_plane_restr0.006201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5004-1.56870.2131310.16862754X-RAY DIFFRACTION99
1.5687-1.65141342787X-RAY DIFFRACTION99
1.6514-1.75480.17881450.1592760X-RAY DIFFRACTION99
1.7548-1.89030.2031340.15452789X-RAY DIFFRACTION99
1.8903-2.08050.20291250.15562777X-RAY DIFFRACTION99
2.0805-2.38140.17871430.15752701X-RAY DIFFRACTION96
2.3814-2.99980.19121470.17972743X-RAY DIFFRACTION97
2.9998-3.180.16961480.15852858X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.514-0.70420.42344.49052.92772.46670.07750.0910.1651-0.15010.1377-0.4453-0.31850.4703-0.30760.1297-0.0649-0.01660.1411-0.00530.1647-6.2741-17.56555.7964
22.99722.2230.63323.89561.80464.3839-0.24030.17680.0244-0.35760.1943-0.054-0.00720.3008-0.01140.11570.00370.02320.12410.00630.0854-7.0582-27.6585-14.7663
31.96390.0693-0.24876.41444.53583.75240.0469-0.1407-0.02560.0757-0.1002-0.07280.0213-0.04740.07030.0544-0.0091-0.00390.05970.0120.0623-8.78-25.30681.8468
40.842-0.68760.41641.26990.41512.66760.0316-0.02440.09580.04350.0321-0.1048-0.06950.1023-0.04460.0875-0.02250.00320.0705-0.01520.0759-16.3294-19.20885.598
51.08490.9286-1.30961.7785-1.60211.82350.21240.28090.3561-0.01250.14360.0608-0.3949-0.26680.32510.18920.04130.06590.11280.04850.129-19.7375-17.2257-6.3264
63.50050.24870.70372.81251.00240.46640.15180.3361-0.2162-0.2882-0.00350.11730.5986-0.10940.12320.1979-0.0137-0.02030.1569-0.01990.1356-23.9022-28.1621-2.1092
71.76370.0666-0.11872.12810.2653.4476-0.00630.04110.03920.0055-0.0449-0.0869-0.06270.04890.05530.04120.0003-0.00870.01620.00680.0441-12.9848-29.2972.3171
80.5306-0.167-1.0750.55190.40473.96830.080.00660.0657-0.10790.023-0.0633-0.1971-0.0226-0.05090.0825-0.00080.00410.06750.01610.0688-14.902-22.1693-8.6655
92.6980.78611.17133.382-0.20946.88460.0382-0.20120.16650.2569-0.02530.13390.113-0.334-0.02640.05610.01560.00470.1079-0.02650.0706-24.9884-19.39478.6325
101.7292-0.4442-0.73110.98570.30453.8592-0.0551-0.05620.1414-0.07310.04640.0491-0.13740.23250.06320.0994-0.03360.00170.02830.01010.0755-13.1354-17.2478-6.1592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 17 )
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 25 )
4X-RAY DIFFRACTION4chain 'A' and (resid 26 through 39 )
5X-RAY DIFFRACTION5chain 'A' and (resid 40 through 52 )
6X-RAY DIFFRACTION6chain 'A' and (resid 53 through 67 )
7X-RAY DIFFRACTION7chain 'A' and (resid 68 through 83 )
8X-RAY DIFFRACTION8chain 'A' and (resid 84 through 99 )
9X-RAY DIFFRACTION9chain 'A' and (resid 100 through 107 )
10X-RAY DIFFRACTION10chain 'A' and (resid 108 through 127 )

+
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