[English] 日本語
Yorodumi
- PDB-6vgo: Crystal Structure of Human Dipeptidase 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vgo
TitleCrystal Structure of Human Dipeptidase 3
ComponentsDipeptidase 3
KeywordsHYDROLASE / Metalloprotease
Function / homology
Function and homology information


LTC4-CYSLTR mediated IL4 production / Aflatoxin activation and detoxification / Synthesis of Leukotrienes (LT) and Eoxins (EX) / dipeptidase activity / acrosomal vesicle / proteolysis / membrane / plasma membrane
Similarity search - Function
Dipeptidase 2/3 / Membrane dipeptidase, active site / Renal dipeptidase active site. / Peptidase M19 / Membrane dipeptidase (Peptidase family M19) / Renal dipeptidase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsHayashi, K. / Longenecker, K.L. / Vivona, S.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structure of human DPEP3 in complex with the SC-003 antibody Fab fragment reveals basis for lack of dipeptidase activity.
Authors: Hayashi, K. / Longenecker, K.L. / Koenig, P. / Prashar, A. / Hampl, J. / Stoll, V. / Vivona, S.
History
DepositionJan 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 11, 2023Group: 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: Dipeptidase 3


Theoretical massNumber of molelcules
Total (without water)53,7451
Polymers53,7451
Non-polymers00
Water3,963220
1
A: Dipeptidase 3

A: Dipeptidase 3


Theoretical massNumber of molelcules
Total (without water)107,4902
Polymers107,4902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2230 Å2
ΔGint-8 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.880, 65.880, 194.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Dipeptidase 3


Mass: 53745.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPEP3, UNQ834/PRO1772 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9H4B8, membrane dipeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.96 Å3/Da / Density % sol: 37.29 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.1 M calcium acetate, 0.1 M sodium acetate pH 4.5, 10% w/v PEG4000

-
Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→62.39 Å / Num. obs: 39548 / % possible obs: 99.8 % / Redundancy: 12.7 % / Rrim(I) all: 0.078 / Net I/σ(I): 18
Reflection shellResolution: 1.82→1.85 Å / Num. unique obs: 1939 / Rpim(I) all: 0.38

-
Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ITQ

1itq


Resolution: 1.82→62.39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.117 / SU Rfree Blow DPI: 0.11 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1997 5.05 %RANDOM
Rwork0.186 ---
obs0.187 39548 99.8 %-
Displacement parametersBiso max: 116.41 Å2 / Biso mean: 39.11 Å2 / Biso min: 24.14 Å2
Baniso -1Baniso -2Baniso -3
1--5.2057 Å20 Å20 Å2
2---5.2057 Å20 Å2
3---10.4115 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.82→62.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 0 220 2952
Biso mean---48.56 -
Num. residues----350
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d987SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes480HARMONIC5
X-RAY DIFFRACTIONt_it2779HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion353SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3512SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2779HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3764HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion14.98
LS refinement shellResolution: 1.82→1.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2279 52 6.57 %
Rwork0.2264 739 -
all0.2265 791 -
obs--99.36 %

+
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://pdbjlvh1.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