[English] 日本語
Yorodumi
- PDB-7f2s: Crystal structure of anti S-gatifloxacin antibody Fab fragment ap... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f2s
TitleCrystal structure of anti S-gatifloxacin antibody Fab fragment apo form
Components(Antibody Fab fragment ...) x 2
KeywordsIMMUNE SYSTEM / antibody / gatifloxacin / Fab fragment / enantioselectivity
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsWang, L.T. / Jiao, W.Y. / Shen, X. / Lei, H.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFC1601700 China
CitationJournal: Rsc Adv / Year: 2021
Title: Conformational adaptability determining antibody recognition to distomer: structure analysis of enantioselective antibody against chiral drug gatifloxacin
Authors: Wang, L.T. / Xie, W. / Jiao, W.Y. / Zhang, C. / Li, X. / Xu, Z. / Huang, X. / Lei, H.T. / Shen, X.
History
DepositionJun 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antibody Fab fragment heavy chain
B: Antibody Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,31923
Polymers47,6022
Non-polymers1,71721
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-95 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.058, 76.058, 378.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-305-

GOL

-
Components

-
Antibody , 2 types, 2 molecules AB

#1: Antibody Antibody Fab fragment heavy chain


Mass: 23473.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Antibody Fab fragment light chain


Mass: 24128.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

-
Non-polymers , 5 types, 58 molecules

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


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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.8 M sodium acetate pH 4.6, 1.6 M ammonium sulfate, 24% glycerol

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.62→47.36 Å / Num. obs: 20813 / % possible obs: 100 % / Redundancy: 36.5 % / Biso Wilson estimate: 77.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.021 / Rrim(I) all: 0.098 / Χ2: 0.99 / Net I/σ(I): 33.6
Reflection shellResolution: 2.62→2.74 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2452 / CC1/2: 0.883 / Χ2: 0.8

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EGJ

1egj


Resolution: 2.62→45.58 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 0.78 / Phase error: 34.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2776 997 4.81 %
Rwork0.2469 35023 -
obs0.2485 20679 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.36 Å2 / Biso mean: 112.671 Å2 / Biso min: 56.77 Å2
Refinement stepCycle: final / Resolution: 2.62→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 104 37 3277
Biso mean--117.17 95.84 -
Num. residues----415
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.62-2.690.43361300.423926892819
2.69-2.770.40341500.404326572807
2.77-2.860.40771520.354726982850
2.86-2.960.40111600.339726612821
2.96-3.080.34781380.330926792817
3.08-3.220.33651280.303627032831
3.22-3.390.33621240.304127062830
3.39-3.60.29331360.244827212857
3.6-3.880.32391000.243127082808
3.88-4.270.2451500.234826942844
4.27-4.890.2411340.1927002834
4.89-6.150.23231270.220927022829
6.16-45.580.24991410.224727052846
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)
10.4133-1.314-0.41393.14930.72473.7103-0.02550.20950.30990.5151-0.1318-0.4436-0.4083-0.160.13530.94650.2776-0.14350.8270.03030.86222.065229.4718-44.5775
22.75760.9734-0.93922.1687-0.23596.71840.09190.05560.38690.37710.26290.2044-0.4616-0.9165-0.37770.63650.2389-0.09820.76360.0970.817110.999230.4565-49.8772
35.3139-0.1519-0.67544.10270.70294.8660.13290.92231.0679-0.9380.2262-0.3369-1.82680.0389-0.33440.85470.1295-0.04610.65870.09310.732520.964534.235-51.3907
41.3825-0.0733-0.35483.3473-0.48521.82190.1091-0.23660.24350.594-0.1822-0.2305-1.0731-1.3125-0.02761.17850.4788-0.13920.81790.07230.84214.88832.6034-40.4295
51.4408-0.53080.54582.58040.65990.9916-0.2021-0.6561-0.02970.6457-0.05530.2812-1.949-1.46680.0471.93960.8887-0.01611.035-0.00570.927117.055129.7644-13.6771
62.01230.05481.24143.8579-0.81911.4689-0.8825-0.74660.21720.7790.5652-0.0191-1.7358-0.97910.37571.7510.6631-0.0471.04370.03220.843518.884528.8769-14.7119
73.11780.2557-1.23172.30060.34914.8745-0.27040.4963-0.0144-0.19430.34230.47150.5557-2.0496-0.2160.8554-0.0742-0.05531.44340.28090.942-1.48518.1423-46.1098
82.0907-0.4106-0.5061.5318-0.06272.37470.6189-0.0353-0.98670.69890.32470.35841.646-0.8809-0.45591.288-0.1275-0.18521.23390.30891.12612.873712.1092-42.859
90.2928-1.24510.49541.7072-0.90394.1344-0.4367-0.53580.19130.940.90240.4302-1.0351-1.5602-0.33921.21250.51670.11671.53390.23490.9153.727626.8632-21.8873
103.86890.2017-0.82422.2572-1.13112.9849-0.2757-1.37920.3681.0946-0.37660.7281-1.3457-1.60650.40681.77260.79540.09822.06570.02690.8843.503930.325-7.4314
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 32 )A1 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 64 )A33 - 64
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 83 )A65 - 83
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 122 )A84 - 122
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 160 )A123 - 160
6X-RAY DIFFRACTION6chain 'A' and (resid 161 through 216 )A161 - 216
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 42 )B1 - 42
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 83 )B43 - 83
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 167 )B84 - 167
10X-RAY DIFFRACTION10chain 'B' and (resid 168 through 215 )B168 - 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