[English] 日本語
Yorodumi
- PDB-4fze: Crystal structure of N26_i1 Fab, an ADCC mediating anti-HIV-1 ant... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fze
TitleCrystal structure of N26_i1 Fab, an ADCC mediating anti-HIV-1 antibody.
Components
  • N26_i1 Fab heavy chain
  • N26_i1 Fab light chain
KeywordsIMMUNE SYSTEM / ADCC / ANTI-HIV-1 ENV ANTIBODY N26_i1 / VIRAL GLYCOPROTEIN GP120 / HIV-1 ENV / CD4I ANTIBODY / FAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsTolbert, W.D. / Wu, X. / Pazgier, M.
CitationJournal: To be Published
Title: Crystal structure of N26_i1 Fab, an ADCC mediating anti-HIV-1 antibody.
Authors: Tolbert, W.D. / Wu, X. / Pazgier, M.
History
DepositionJul 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3May 19, 2021Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Sep 13, 2023Group: 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: N26_i1 Fab light chain
H: N26_i1 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,0682
Polymers47,0682
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-25 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.636, 124.452, 41.433
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-362-

HOH

21L-400-

HOH

31H-397-

HOH

-
Components

#1: Antibody N26_i1 Fab light chain


Mass: 22514.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody N26_i1 Fab heavy chain


Mass: 24553.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo Sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5, and 30% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2012 / Details: Rh coated flat mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. all: 32431 / Num. obs: 32042 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.838 / Mean I/σ(I) obs: 1.1 / Num. unique all: 2748 / % possible all: 86

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
PHASERphasing
CNS(phenix.refine: 1.8_1069)refinement
REFMAC(phenix.refine: 1.8_1069)refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D9L

4d9l


Resolution: 1.999→41.088 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 3202 10 %RANDOM
Rwork0.1856 ---
all0.1913 32446 --
obs0.1913 32031 98.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.999→41.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 0 252 3461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073290
X-RAY DIFFRACTIONf_angle_d1.1454489
X-RAY DIFFRACTIONf_dihedral_angle_d14.2191158
X-RAY DIFFRACTIONf_chiral_restr0.071519
X-RAY DIFFRACTIONf_plane_restr0.005571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9992-2.0290.35241240.33481064X-RAY DIFFRACTION84
2.029-2.06080.35671350.30261138X-RAY DIFFRACTION91
2.0608-2.09450.34141260.29241235X-RAY DIFFRACTION97
2.0945-2.13070.3271310.28131261X-RAY DIFFRACTION100
2.1307-2.16940.28111450.27231279X-RAY DIFFRACTION100
2.1694-2.21110.35221280.25911272X-RAY DIFFRACTION100
2.2111-2.25620.32951520.24591252X-RAY DIFFRACTION100
2.2562-2.30530.30381510.25181277X-RAY DIFFRACTION100
2.3053-2.35890.28651280.22951242X-RAY DIFFRACTION100
2.3589-2.41790.26811570.21681261X-RAY DIFFRACTION100
2.4179-2.48330.26811820.2171226X-RAY DIFFRACTION100
2.4833-2.55630.31071380.21771255X-RAY DIFFRACTION100
2.5563-2.63880.29611530.20151256X-RAY DIFFRACTION100
2.6388-2.73310.26371400.19711283X-RAY DIFFRACTION100
2.7331-2.84250.26191530.18751254X-RAY DIFFRACTION100
2.8425-2.97190.26951470.19081267X-RAY DIFFRACTION100
2.9719-3.12850.26651520.18341260X-RAY DIFFRACTION100
3.1285-3.32440.24771180.17541280X-RAY DIFFRACTION100
3.3244-3.5810.19721470.16631270X-RAY DIFFRACTION100
3.581-3.94110.20691020.15841314X-RAY DIFFRACTION100
3.9411-4.51080.18151330.13721283X-RAY DIFFRACTION100
4.5108-5.68070.19141330.13511292X-RAY DIFFRACTION100
5.6807-41.09680.20161270.16631308X-RAY DIFFRACTION100
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)
11.5762-0.13160.04471.785-1.20691.39790.04870.0773-0.0325-0.0059-0.0620.00390.02540.06680.03550.13820.00250.01380.1469-0.06490.1676-14.922113.121710.0222
22.3026-0.85540.49731.3185-0.99741.6003-0.0077-0.07780.09120.0690.08740.1146-0.0566-0.122-0.05890.15420.00560.01670.1509-0.07450.1456-32.245117.974112.6859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 2 through 210 )
2X-RAY DIFFRACTION2chain 'H' and (resid 1 through 215 )

+
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