[English] 日本語
Yorodumi
- PDB-1kfa: Crystal structure of Fab fragment complexed with gibberellin A4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kfa
TitleCrystal structure of Fab fragment complexed with gibberellin A4
Components
  • monoclonal antibody heavy chain
  • monoclonal antibody light chain
KeywordsIMMUNE SYSTEM / Immunoglobuiln fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / GIBBERELLIN A4
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMurata, T. / Fushinobu, S. / Nakajima, M. / Asami, O. / Sassa, T. / Wakagi, T. / Yamaguchi, I.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2002
Title: Crystal structure of the liganded anti-gibberellin A(4) antibody 4-B8(8)/E9 Fab fragment.
Authors: Murata, T. / Fushinobu, S. / Nakajima, M. / Asami, O. / Sassa, T. / Wakagi, T. / Yamaguchi, I.
#1: Journal: PLANT CELL.PHYSIOL. / Year: 1991
Title: Monoclonal antibodies specific for non-derivatized gibberellins I
Authors: Nakajima, M. / Yamaguchi, I. / Nagatani, A. / Kizawa, S. / Murofushi, N. / Furuya, N. / Takahashi, N.
History
DepositionNov 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 25, 2013Group: Source and taxonomy
Revision 1.4Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: monoclonal antibody light chain
H: monoclonal antibody heavy chain
M: monoclonal antibody light chain
I: monoclonal antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6956
Polymers95,0304
Non-polymers6652
Water2,126118
1
L: monoclonal antibody light chain
H: monoclonal antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8483
Polymers47,5152
Non-polymers3321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-28 kcal/mol
Surface area18950 Å2
MethodPISA
2
M: monoclonal antibody light chain
I: monoclonal antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8483
Polymers47,5152
Non-polymers3321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-27 kcal/mol
Surface area18540 Å2
MethodPISA
3
L: monoclonal antibody light chain
H: monoclonal antibody heavy chain
hetero molecules

M: monoclonal antibody light chain
I: monoclonal antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6956
Polymers95,0304
Non-polymers6652
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area9590 Å2
ΔGint-62 kcal/mol
Surface area35910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.076, 150.146, 106.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Antibody monoclonal antibody light chain /


Mass: 23754.285 Da / Num. of mol.: 2 / Fragment: residues 1-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Genus: Homo / Cell (production host): Hybridoma cell / Cellular location (production host): ascitic fluid / Production host: Mus musculus (house mouse)
#2: Antibody monoclonal antibody heavy chain /


Mass: 23760.887 Da / Num. of mol.: 2 / Fragment: Variable domain, constant domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Genus: Homo / Cell (production host): Hybridoma cell / Cellular location (production host): ascitic fluid / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-GA4 / GIBBERELLIN A4 / Gibberellin


Mass: 332.391 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24O5 / Comment: hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 303K
Crystal grow
*PLUS
Temperature: 30 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %(v/v)glycerol1reservoir
212 %(w/v)PEG33501reservoir
30.06 MBis-Tris-HCl1reservoirpH6.5
48 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→39.62 Å / Num. all: 402565 / Num. obs: 402565 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 7.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3799 / Rsym value: 0.321 / % possible all: 99.7
Reflection
*PLUS
Num. obs: 26460 / % possible obs: 100 % / Num. measured all: 402565
Reflection shell
*PLUS
Highest resolution: 2.7 Å / % possible obs: 100 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ikf

1ikf


Resolution: 2.8→39.62 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1685086.35 / Data cutoff low absF: 0 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1192 5 %random
Rwork0.235 ---
all0.243 26440 --
obs0.261 23741 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.0048 Å2 / ksol: 0.373888 e/Å3
Displacement parametersBiso mean: 40.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---0.94 Å20 Å2
3----0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6511 0 48 118 6677
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 194 5 %
Rwork0.242 --
obs-3709 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ga4.paramga4.top
Refinement
*PLUS
Highest resolution: 2.8 Å / Num. reflection obs: 22549 / % reflection Rfree: 5 % / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1

+
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