[English] 日本語
Yorodumi
- PDB-4jo4: Crystal structure of rabbit mAb R20 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jo4
TitleCrystal structure of rabbit mAb R20 Fab
Components
  • monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain
  • monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain
KeywordsIMMUNE SYSTEM / Ig / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsPan, R.M. / Kong, X.P.
CitationJournal: J.Virol. / Year: 2013
Title: Rabbit Anti-HIV-1 Monoclonal Antibodies Raised by Immunization Can Mimic the Antigen-Binding Modes of Antibodies Derived from HIV-1-Infected Humans.
Authors: Pan, R. / Sampson, J.M. / Chen, Y. / Vaine, M. / Wang, S. / Lu, S. / Kong, X.P.
History
DepositionMar 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain
H: monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain
M: monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain
I: monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8789
Polymers92,9714
Non-polymers9075
Water13,151730
1
L: monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain
H: monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8204
Polymers46,4862
Non-polymers3342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-46 kcal/mol
Surface area18970 Å2
MethodPISA
2
M: monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain
I: monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0585
Polymers46,4862
Non-polymers5733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-42 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.649, 119.690, 135.337
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain


Mass: 22596.881 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain


Mass: 23888.824 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human) / Keywords: Fab
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Keywords: 2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 730 / 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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4 M ammonium sulfate, 1.7% PEG400, 85 mM HEPES, pH 7.5, 15% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2012
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→38.27 Å / Num. all: 53673 / Num. obs: 53548 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.175 / Rsym value: 0.107 / Net I/σ(I): 22.55
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.105 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.593 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
Blu-Icelikedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→38.268 Å / SU ML: 0.32 / σ(F): 0.23 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 2700 5.04 %RANDOM
Rwork0.1843 ---
obs0.1864 53548 99.58 %-
all-53673 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.892 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1675 Å20 Å2-0 Å2
2--1.9573 Å20 Å2
3----2.1248 Å2
Refinement stepCycle: LAST / Resolution: 2.27→38.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6520 0 46 730 7296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086721
X-RAY DIFFRACTIONf_angle_d1.0889174
X-RAY DIFFRACTIONf_dihedral_angle_d14.9542319
X-RAY DIFFRACTIONf_chiral_restr0.071088
X-RAY DIFFRACTIONf_plane_restr0.0041162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.31130.30841410.23792624X-RAY DIFFRACTION99
2.3113-2.35570.3311360.23132642X-RAY DIFFRACTION99
2.3557-2.40380.2871420.2362626X-RAY DIFFRACTION100
2.4038-2.45610.29751330.23322647X-RAY DIFFRACTION99
2.4561-2.51320.29691630.23252636X-RAY DIFFRACTION100
2.5132-2.5760.31821180.22522673X-RAY DIFFRACTION100
2.576-2.64570.28171550.21192636X-RAY DIFFRACTION100
2.6457-2.72350.27451500.21292643X-RAY DIFFRACTION100
2.7235-2.81140.26971230.21432653X-RAY DIFFRACTION100
2.8114-2.91180.25561200.20212666X-RAY DIFFRACTION100
2.9118-3.02830.22191350.18912669X-RAY DIFFRACTION100
3.0283-3.16610.23851470.19112671X-RAY DIFFRACTION100
3.1661-3.33290.22641410.1882677X-RAY DIFFRACTION100
3.3329-3.54160.22161430.17982685X-RAY DIFFRACTION100
3.5416-3.81480.19751510.17242670X-RAY DIFFRACTION100
3.8148-4.19830.2031440.15182700X-RAY DIFFRACTION100
4.1983-4.80480.16251480.13192720X-RAY DIFFRACTION100
4.8048-6.04970.17651460.15122758X-RAY DIFFRACTION100
6.0497-38.27390.20251640.19262852X-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