[English] 日本語
Yorodumi
- PDB-3wif: Crystal structure of anti-prostaglandin E2 Fab fragment 9Cl-PGF2b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wif
TitleCrystal structure of anti-prostaglandin E2 Fab fragment 9Cl-PGF2beta complex
Components
  • mAb Fab H fragment
  • mAb Fab L fragment
KeywordsIMMUNE SYSTEM / immunogloblin / Anti-Prostaglandin E2 antibody / Prostaglandin E2
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-ON5
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSugahara, M. / Ago, H. / Saino, H. / Miyano, M.
CitationJournal: To be Published
Title: Crystal structure of anti-Prostaglandin E2 Fab fragment with Prostaglandin E2
Authors: Sugahara, M. / Ago, H. / Saino, H. / Miyano, M. / Kurahashi, Y. / Aoyama, S. / Takehira, M. / Yutani, K. / Yamamoto, S.
History
DepositionSep 12, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 17, 2014Provider: 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 / 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
Revision 1.2Oct 30, 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: mAb Fab H fragment
B: mAb Fab L fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7783
Polymers47,4052
Non-polymers3731
Water13,403744
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-22 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.660, 82.310, 82.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody mAb Fab H fragment


Mass: 23511.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: Hybridoma
#2: Antibody mAb Fab L fragment


Mass: 23893.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: Hybridoma
#3: Chemical ChemComp-ON5 / (Z)-7-[(1R,2R,3R,5R)-5-chloranyl-3-oxidanyl-2-[(E,3S)-3-oxidanyloct-1-enyl]cyclopentyl]hept-5-enoic acid


Mass: 372.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H33ClO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 744 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE REFERENCE SEQUENCE OF CHAIN A IS BAL50003 AND CHAIN B IS BAL50004 IN GENBANK.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 293 K / Method: oil microbatch / pH: 5
Details: 0.1M Na acetate, 25%(w/v) PEG3350, pH 5.0, OIL MICROBATCH, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 25, 2009
RadiationMonochromator: SI(111) DOUBL CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→35.64 Å / Num. obs: 53235 / % possible obs: 99.2 % / Redundancy: 7 % / Rmerge(I) obs: 0.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.8 / Num. unique all: 7287 / % possible all: 94.4

-
Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DDQ

2ddq


Resolution: 1.7→35.33 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8959 / SU ML: 0.18 / σ(F): 1.4 / Phase error: 17.19 / Stereochemistry target values: ML
Details: The structure was refined also with REFMAC5 and CNS
RfactorNum. reflection% reflection
Rfree0.1898 2700 5.08 %
Rwork0.172 --
obs0.1729 53162 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.11 Å2 / Biso mean: 20.8515 Å2 / Biso min: 3.63 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3253 0 25 744 4022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053435
X-RAY DIFFRACTIONf_angle_d1.0354684
X-RAY DIFFRACTIONf_chiral_restr0.071530
X-RAY DIFFRACTIONf_plane_restr0.005596
X-RAY DIFFRACTIONf_dihedral_angle_d11.9151203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.76080.2472550.22864634488992
1.7608-1.83130.21882450.1964984522999
1.8313-1.91470.21632800.188850215301100
1.9147-2.01560.19542870.178250375324100
2.0156-2.14190.19332630.17650265289100
2.1419-2.30720.1962810.175150525333100
2.3072-2.53940.19972730.177750775350100
2.5394-2.90670.20662800.179251085388100
2.9067-3.66150.17172640.163651635427100
3.6615-35.33760.16382720.150953605632100

+
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