[English] 日本語
Yorodumi
- PDB-3qrg: Crystal structure of antiRSVF Fab B21m -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qrg
TitleCrystal structure of antiRSVF Fab B21m
Components
  • Fab heavy chain Fd fragment
  • Fab light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / Fab structure / RSV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsLuo, J. / Tsui, P. / Lewandowski, F. / Spurlino, J. / Vecchio, F.D.
CitationJournal: To be Published
Title: Crystal structure anti-RSV Fab B21m
Authors: Luo, J. / Tsui, P. / Lewandowski, F. / Spurlino, J. / Vecchio, F.D.
History
DepositionFeb 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_mod_residue
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Fab light chain
H: Fab heavy chain Fd fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,74126
Polymers48,3582
Non-polymers2,38324
Water10,791599
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-189 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.412, 166.412, 166.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

-
Components

-
Antibody , 2 types, 2 molecules LH

#1: Antibody Fab light chain / Fragment antigen-binding


Mass: 23921.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cell (production host): HUMAN EMBRYONIC KIDNEY (HEK) 293 CELLS
Production host: HOMO SAPIENS (human)
#2: Antibody Fab heavy chain Fd fragment


Mass: 24436.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cell (production host): HUMAN EMBRYONIC KIDNEY (HEK) 293 CELLS
Production host: HOMO SAPIENS (human)

-
Non-polymers , 4 types, 623 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 3.97 Å3/Da / Density % sol: 69.02 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M BisTris, 2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 4, 2005
RadiationMonochromator: Accel Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 83331 / Num. obs: 83331 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7_650)refinement
CNXrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.699→41.603 Å / SU ML: 0.21 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1847 4167 5.01 %Random
Rwork0.1609 ---
obs0.162 83118 99.07 %-
all-83331 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.003 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3164 Å20 Å20 Å2
2--0.3164 Å20 Å2
3---0.3164 Å2
Refinement stepCycle: LAST / Resolution: 1.699→41.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 138 599 4073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0263715
X-RAY DIFFRACTIONf_angle_d2.3965110
X-RAY DIFFRACTIONf_dihedral_angle_d14.1811390
X-RAY DIFFRACTIONf_chiral_restr0.213580
X-RAY DIFFRACTIONf_plane_restr0.012635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6991-1.71850.28821420.2722461X-RAY DIFFRACTION93
1.7185-1.73870.26171260.24192488X-RAY DIFFRACTION94
1.7387-1.75990.25791270.23812542X-RAY DIFFRACTION96
1.7599-1.78220.29291490.22722537X-RAY DIFFRACTION97
1.7822-1.80560.2441350.20722584X-RAY DIFFRACTION98
1.8056-1.83030.28691290.20572624X-RAY DIFFRACTION99
1.8303-1.85650.24311530.20532622X-RAY DIFFRACTION100
1.8565-1.88420.2451350.19252614X-RAY DIFFRACTION100
1.8842-1.91360.23361450.19782659X-RAY DIFFRACTION100
1.9136-1.9450.19121250.17752653X-RAY DIFFRACTION100
1.945-1.97850.20461520.17232629X-RAY DIFFRACTION100
1.9785-2.01450.1991300.15892660X-RAY DIFFRACTION100
2.0145-2.05330.17281450.15682598X-RAY DIFFRACTION100
2.0533-2.09520.16151350.14812650X-RAY DIFFRACTION100
2.0952-2.14070.18651230.15542669X-RAY DIFFRACTION100
2.1407-2.19050.19951250.16312663X-RAY DIFFRACTION100
2.1905-2.24530.19261420.15642615X-RAY DIFFRACTION100
2.2453-2.3060.18091560.15812617X-RAY DIFFRACTION100
2.306-2.37390.19441470.1672615X-RAY DIFFRACTION100
2.3739-2.45050.20471270.16642695X-RAY DIFFRACTION100
2.4505-2.5380.21811130.16682651X-RAY DIFFRACTION100
2.538-2.63970.21550.1572626X-RAY DIFFRACTION100
2.6397-2.75980.1971570.16122647X-RAY DIFFRACTION100
2.7598-2.90520.14981470.15432668X-RAY DIFFRACTION100
2.9052-3.08720.17541440.1512655X-RAY DIFFRACTION100
3.0872-3.32550.14521440.14962654X-RAY DIFFRACTION100
3.3255-3.65990.15951410.14322671X-RAY DIFFRACTION100
3.6599-4.18910.15111320.12892694X-RAY DIFFRACTION100
4.1891-5.27620.14031190.122730X-RAY DIFFRACTION100
5.2762-41.61550.20541670.20882760X-RAY DIFFRACTION100

+
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