[English] 日本語
Yorodumi
- PDB-4z0b: Crystal Structure of the Fab Fragment of Anti-ofloxacin Antibody ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z0b
TitleCrystal Structure of the Fab Fragment of Anti-ofloxacin Antibody and Exploration Its Receptor Binding Site
Components
  • antibody heavy chain
  • antibody light chain
KeywordsIMMUNE SYSTEM / Ofloxacin ELISA Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHe, K. / Du, X. / Sheng, W. / Zhou, X. / Wang, J. / Wang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National naural science foundation of china31225021 China
CitationJournal: J.Agric.Food Chem. / Year: 2016
Title: Crystal Structure of the Fab Fragment of an Anti-ofloxacin Antibody and Exploration of Its Specific Binding.
Authors: He, K. / Du, X. / Sheng, W. / Zhou, X. / Wang, J. / Wang, S.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: antibody heavy chain
L: antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6473
Polymers46,5522
Non-polymers951
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-25 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.828, 53.528, 129.103
Angle α, β, γ (deg.)90.000, 98.390, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody antibody heavy chain


Mass: 23826.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
#2: Antibody antibody light chain


Mass: 22725.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.2M ammonium phosphate dibasic, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 7100 / % possible obs: 90 % / Redundancy: 2.9 % / Net I/σ(I): 9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AR1

1ar1


Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.84 / Cor.coef. Fo:Fc free: 0.806 / SU B: 37.959 / SU ML: 0.608 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.774 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3086 272 4.4 %RANDOM
Rwork0.276 ---
obs0.2775 5895 85.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.5 Å2 / Biso mean: 55.508 Å2 / Biso min: 35.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å20.15 Å2
2---0.85 Å20 Å2
3----1.62 Å2
Refinement stepCycle: final / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 5 0 3174
Biso mean--59.19 --
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.023252
X-RAY DIFFRACTIONr_bond_other_d0.0010.022881
X-RAY DIFFRACTIONr_angle_refined_deg0.941.9474430
X-RAY DIFFRACTIONr_angle_other_deg0.6636691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4525421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30324.083120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64715499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7341512
X-RAY DIFFRACTIONr_chiral_restr0.0520.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02714
X-RAY DIFFRACTIONr_mcbond_it0.7255.7211693
X-RAY DIFFRACTIONr_mcbond_other0.7255.7211692
X-RAY DIFFRACTIONr_mcangle_it1.3668.5782111
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 9 -
Rwork0.361 245 -
all-254 -
obs--51.11 %

+
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