[English] 日本語
Yorodumi
- PDB-5d8i: Engineering the Species-Specificity of an Inhibitory Antibody Tar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d8i
TitleEngineering the Species-Specificity of an Inhibitory Antibody Targeting a Modulator of Tumor Stroma
ComponentsSulfhydryl oxidase 1Oxidase
KeywordsOXIDOREDUCTASE / enzyme / disulfide bonds / thioredoxin fold
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Platelet degranulation / negative regulation of macroautophagy / intercellular bridge / protein disulfide isomerase activity / Neutrophil degranulation ...flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Platelet degranulation / negative regulation of macroautophagy / intercellular bridge / protein disulfide isomerase activity / Neutrophil degranulation / FAD binding / protein folding / Golgi membrane / intracellular membrane-bounded organelle / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome
Similarity search - Function
Sulfhydryl oxidase, flavin adenine dinucleotide (FAD) binding domain / Sulfhydryl oxidase, Trx-like domain / Sulfhydryl oxidase, flavin adenine dinucleotide (FAD) binding domain superfamily / QSOX Trx-like domain / Flavin adenine dinucleotide (FAD)-dependent sulfhydryl oxidase / Sulfhydryl oxidase / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain superfamily / Erv1 / Alr family / ERV/ALR sulfhydryl oxidase domain profile. ...Sulfhydryl oxidase, flavin adenine dinucleotide (FAD) binding domain / Sulfhydryl oxidase, Trx-like domain / Sulfhydryl oxidase, flavin adenine dinucleotide (FAD) binding domain superfamily / QSOX Trx-like domain / Flavin adenine dinucleotide (FAD)-dependent sulfhydryl oxidase / Sulfhydryl oxidase / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain superfamily / Erv1 / Alr family / ERV/ALR sulfhydryl oxidase domain profile. / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sulfhydryl oxidase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGrossman, I. / Fass, D.
Funding support1items
OrganizationGrant numberCountry
European Research Council310649
CitationJournal: Protein Eng.Des.Sel. / Year: 2016
Title: Overcoming a species-specificity barrier in development of an inhibitory antibody targeting a modulator of tumor stroma.
Authors: Grossman, I. / Ilani, T. / Fleishman, S.J. / Fass, D.
History
DepositionAug 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfhydryl oxidase 1
B: Sulfhydryl oxidase 1


Theoretical massNumber of molelcules
Total (without water)53,1842
Polymers53,1842
Non-polymers00
Water5,152286
1
A: Sulfhydryl oxidase 1


Theoretical massNumber of molelcules
Total (without water)26,5921
Polymers26,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfhydryl oxidase 1


Theoretical massNumber of molelcules
Total (without water)26,5921
Polymers26,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.480, 116.375, 50.023
Angle α, β, γ (deg.)90.00, 103.09, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Sulfhydryl oxidase 1 / Oxidase / mSOx / Quiescin Q6 / Skin sulfhydryl oxidase


Mass: 26591.994 Da / Num. of mol.: 2 / Fragment: UNP residues 36-275
Source method: isolated from a genetically manipulated source
Details: SVLYSSSDPLTLLDADSVRPTVLGSSSAWAVEFFA SWCGHCIAFAPTWKELANDVKDWRPALNLAVLDCAEETNSAVCREFNIAGFPTVRFFQAFTKNGSGATLP GAGANVQTLRMRLIDALESHRDTWPPACPPLEPAKLNDIDGFFTRNKADYLALVFEREDSYLGREVTLDL ...Details: SVLYSSSDPLTLLDADSVRPTVLGSSSAWAVEFFA SWCGHCIAFAPTWKELANDVKDWRPALNLAVLDCAEETNSAVCREFNIAGFPTVRFFQAFTKNGSGATLP GAGANVQTLRMRLIDALESHRDTWPPACPPLEPAKLNDIDGFFTRNKADYLALVFEREDSYLGREVTLDL SQYHAVAVRRVLNTESDLVNKFGVTDFPSCYLLLRNGSVSRVPVLVESRSFYTSYLRGLPGLTRD
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qsox1, Qscn6, Sox / Plasmid: pet15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8BND5, thiol oxidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 5% w/v dimethyl sulfoxide, 0.1 M sodium acetate, pH 4.6, 7% w/v PEG monomethyl ether 2 kD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 28528 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 11.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.2 / % possible all: 79.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6O

3q6o


Resolution: 2.05→28.513 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 27.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 1957 6.87 %random selection
Rwork0.201 ---
obs0.2045 28485 95.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.5 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 0 286 3993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063881
X-RAY DIFFRACTIONf_angle_d1.2755304
X-RAY DIFFRACTIONf_dihedral_angle_d11.91390
X-RAY DIFFRACTIONf_chiral_restr0.094592
X-RAY DIFFRACTIONf_plane_restr0.007698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0474-2.09860.31521050.27441556X-RAY DIFFRACTION78
2.0986-2.15530.28821120.2591765X-RAY DIFFRACTION89
2.1553-2.21870.32861430.25641821X-RAY DIFFRACTION92
2.2187-2.29030.28331330.24611872X-RAY DIFFRACTION95
2.2903-2.37210.29991650.22191893X-RAY DIFFRACTION97
2.3721-2.4670.28381380.22421916X-RAY DIFFRACTION98
2.467-2.57930.28681490.21191918X-RAY DIFFRACTION98
2.5793-2.71510.28591490.21141940X-RAY DIFFRACTION98
2.7151-2.88510.31151420.23371978X-RAY DIFFRACTION99
2.8851-3.10760.25741450.21051928X-RAY DIFFRACTION98
3.1076-3.41990.25211460.20991965X-RAY DIFFRACTION99
3.4199-3.91370.23931530.18231967X-RAY DIFFRACTION99
3.9137-4.92660.22041490.16061986X-RAY DIFFRACTION100
4.9266-28.51620.17791280.17462023X-RAY DIFFRACTION100

+
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