[English] 日本語
Yorodumi
- PDB-3q6g: Crystal structure of Fab of rhesus mAb 2.5B specific for quaterna... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q6g
TitleCrystal structure of Fab of rhesus mAb 2.5B specific for quaternary neutralizing epitope of HIV-1 gp120
Components
  • Heavy chain of Fab of rhesus mAb 2.5B
  • Light chain of Fab of rhesus mAb 2.5B
KeywordsIMMUNE SYSTEM / Ig / neutralization of HIV-1 viruses / Quaternary epitope of HIV-1 gp120
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsSpurrier, B. / Sampson, J. / Totrov, M. / Li, H. / O'Neal, T. / William, C. / Robinson, J. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.
CitationJournal: Structure / Year: 2011
Title: Structural Analysis of Human and Macaque mAbs 2909 and 2.5B: Implications for the Configuration of the Quaternary Neutralizing Epitope of HIV-1 gp120.
Authors: Spurrier, B. / Sampson, J.M. / Totrov, M. / Li, H. / O'Neal, T. / Williams, C. / Robinson, J. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.
History
DepositionDec 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2013Group: Source and taxonomy
Revision 1.3Oct 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
L: Light chain of Fab of rhesus mAb 2.5B
H: Heavy chain of Fab of rhesus mAb 2.5B
M: Light chain of Fab of rhesus mAb 2.5B
I: Heavy chain of Fab of rhesus mAb 2.5B


Theoretical massNumber of molelcules
Total (without water)93,9224
Polymers93,9224
Non-polymers00
Water15,655869
1
L: Light chain of Fab of rhesus mAb 2.5B
H: Heavy chain of Fab of rhesus mAb 2.5B


Theoretical massNumber of molelcules
Total (without water)46,9612
Polymers46,9612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-24 kcal/mol
Surface area20710 Å2
MethodPISA
2
M: Light chain of Fab of rhesus mAb 2.5B
I: Heavy chain of Fab of rhesus mAb 2.5B


Theoretical massNumber of molelcules
Total (without water)46,9612
Polymers46,9612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-25 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.836, 72.817, 88.898
Angle α, β, γ (deg.)90.00, 115.64, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody Light chain of Fab of rhesus mAb 2.5B


Mass: 22180.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Macaca mulatta (Rhesus monkey)
#2: Antibody Heavy chain of Fab of rhesus mAb 2.5B


Mass: 24780.408 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Macaca mulatta (Rhesus monkey)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 869 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 18% PEG 3350, 100 mM ammonium nitrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11.0332
SYNCHROTRONNSLS X6A21
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2009 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
211
ReflectionResolution: 1.9→50 Å / Num. obs: 68825 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.85 / Net I/σ(I): 17.8
Reflection shellResolution: 1.9→1.97 Å / % possible all: 92.8

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.902→29.702 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 3482 5.06 %Random
Rwork0.1909 ---
obs0.193 68825 97.68 %-
all-68825 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.299 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6607 Å2-0 Å20.3776 Å2
2---0.2947 Å20 Å2
3----0.3661 Å2
Refinement stepCycle: LAST / Resolution: 1.902→29.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6554 0 0 869 7423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076712
X-RAY DIFFRACTIONf_angle_d1.1239149
X-RAY DIFFRACTIONf_dihedral_angle_d13.6282362
X-RAY DIFFRACTIONf_chiral_restr0.0781049
X-RAY DIFFRACTIONf_plane_restr0.0051174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9019-1.96990.29473290.26185939X-RAY DIFFRACTION90
1.9699-2.04880.28173100.23036359X-RAY DIFFRACTION95
2.0488-2.1420.25113550.21326400X-RAY DIFFRACTION97
2.142-2.25490.26833440.21296550X-RAY DIFFRACTION98
2.2549-2.39610.26083590.20816577X-RAY DIFFRACTION99
2.3961-2.5810.27463520.216645X-RAY DIFFRACTION99
2.581-2.84060.25573520.20496669X-RAY DIFFRACTION100
2.8406-3.25120.22913320.18836712X-RAY DIFFRACTION100
3.2512-4.09440.19484000.16666697X-RAY DIFFRACTION100
4.0944-29.7060.19413490.16526786X-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