[English] 日本語
Yorodumi
- PDB-6w73: Fab Structure of CD4 Binding Site (CD4bs) Huamn Monoclonal Antibo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w73
TitleFab Structure of CD4 Binding Site (CD4bs) Huamn Monoclonal Antibody HmAb64
Components
  • HmAb64 fab heavy chain
  • HmAb64 fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 gp120 / antibody / IgG
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKong, X. / Pan, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145655 United States
CitationJournal: To Be Published
Title: A CD4 Binding Site (CD4bs) Monoclonal Antibody Elicited from A Human Volunteer Immunized by a DNA Prime/Protein Boost gp120 HIV Vaccine
Authors: Kong, X. / Pan, R.
History
DepositionMar 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: HmAb64 fab light chain
H: HmAb64 fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4584
Polymers47,3782
Non-polymers802
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-36 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.790, 59.352, 75.571
Angle α, β, γ (deg.)90.000, 96.215, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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

#1: Antibody HmAb64 fab light chain


Mass: 23353.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody HmAb64 fab heavy chain


Mass: 24023.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 30% PEG1500, 8%MPD, 0.1M Tris pH8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→45.63 Å / Num. obs: 21339 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 48.4 Å2 / CC1/2: 0.995 / Net I/σ(I): 11.6
Reflection shellResolution: 2.8→2.97 Å / Mean I/σ(I) obs: 2.84 / Num. unique obs: 1621 / CC1/2: 0.882 / Rrim(I) all: 0.53

-
Processing

Software
NameVersionClassification
XDS1.16_3549data processing
XDS1.16_3549data scaling
XDSdata reduction
PHENIXphasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DEE

1dee


Resolution: 2.8→45.63 Å / SU ML: 0.4188 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.074
RfactorNum. reflection% reflection
Rfree0.2627 978 5.01 %
Rwork0.1782 --
obs0.1822 19529 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.61 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 2 32 3342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773384
X-RAY DIFFRACTIONf_angle_d0.9744610
X-RAY DIFFRACTIONf_chiral_restr0.0526528
X-RAY DIFFRACTIONf_plane_restr0.0101585
X-RAY DIFFRACTIONf_dihedral_angle_d16.31172031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.950.35231410.25422664X-RAY DIFFRACTION99.89
2.95-3.130.3621370.23612650X-RAY DIFFRACTION99.71
3.13-3.370.26861410.21132642X-RAY DIFFRACTION99.89
3.37-3.710.2641400.17562664X-RAY DIFFRACTION99.82
3.71-4.250.26551380.15872650X-RAY DIFFRACTION99.93
4.25-5.350.20151390.13532641X-RAY DIFFRACTION100
5.35-45.630.25951420.18042640X-RAY DIFFRACTION99.57

+
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