[English] 日本語
Yorodumi
- PDB-6jci: Crystal structure of Prolyl Endopeptidase from Haliotis discus ha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jci
TitleCrystal structure of Prolyl Endopeptidase from Haliotis discus hannai with SUAM-14746
ComponentsProlyl endopeptidase
KeywordsHYDROLASE / Serine protease family
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H ...Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-BKO / Prolyl endopeptidase
Similarity search - Component
Biological speciesHaliotis discus hannai (Japanese disc abalone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.493 Å
AuthorsLi, W. / Cao, M.
CitationJournal: To Be Published
Title: Crystal structure of Haliotis discus hannai Prolyl Endopeptidase
Authors: Li, W. / Cao, M.
History
DepositionJan 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5314
Polymers85,8801
Non-polymers6513
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-0 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.570, 104.840, 137.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Prolyl endopeptidase /


Mass: 85880.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliotis discus hannai (Japanese disc abalone)
Tissue: MuscleSkeletal muscle / Gene: PREP / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1X9T5X9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-BKO / 1-[4-oxidanyl-2-(1,3-thiazolidin-3-ylcarbonyl)pyrrolidin-1-yl]-4-[2-[(~{E})-2-phenylethenyl]phenoxy]butan-1-one


Mass: 466.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H30N2O4S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.26 Å3/Da / Density % sol: 45.58 % / Description: Rod like
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.65 / Details: 22% PEG3350,0.2 M ammonium citrate dibasic / PH range: 6.0 - 7.5

-
Data collection

DiffractionMean temperature: 195 K / Ambient temp details: Nitrogen steam / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 125569 / % possible obs: 99.1 % / Redundancy: 6.41 % / CC1/2: 0.999 / Rrim(I) all: 0.065 / Net I/σ(I): 18.03
Reflection shellResolution: 1.49→1.53 Å / Redundancy: 5.84 % / Num. unique obs: 8856 / CC1/2: 0.716 / Rrim(I) all: 1 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QFS

1qfs


Resolution: 1.493→49.003 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 6278 5 %
Rwork0.1783 --
obs0.1791 125545 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.493→49.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5657 0 45 407 6109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035871
X-RAY DIFFRACTIONf_angle_d0.6477949
X-RAY DIFFRACTIONf_dihedral_angle_d16.2673479
X-RAY DIFFRACTIONf_chiral_restr0.075832
X-RAY DIFFRACTIONf_plane_restr0.0041029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.493-1.510.33451900.32953610X-RAY DIFFRACTION92
1.51-1.52770.31022070.30173934X-RAY DIFFRACTION99
1.5277-1.54640.31762050.27923889X-RAY DIFFRACTION98
1.5464-1.5660.27672050.26123906X-RAY DIFFRACTION99
1.566-1.58660.26632070.24033924X-RAY DIFFRACTION99
1.5866-1.60830.26182060.2293908X-RAY DIFFRACTION99
1.6083-1.63130.22792090.21153965X-RAY DIFFRACTION99
1.6313-1.65560.22772050.19643909X-RAY DIFFRACTION99
1.6556-1.68150.23052100.19563972X-RAY DIFFRACTION99
1.6815-1.70910.24862050.19283900X-RAY DIFFRACTION99
1.7091-1.73850.22132080.1893953X-RAY DIFFRACTION99
1.7385-1.77010.22362080.18693958X-RAY DIFFRACTION99
1.7701-1.80420.19692100.18883981X-RAY DIFFRACTION99
1.8042-1.8410.18852070.1743950X-RAY DIFFRACTION99
1.841-1.88110.1782080.17533945X-RAY DIFFRACTION100
1.8811-1.92480.21152090.17083992X-RAY DIFFRACTION99
1.9248-1.9730.18642110.16773983X-RAY DIFFRACTION99
1.973-2.02630.15772070.15833958X-RAY DIFFRACTION100
2.0263-2.08590.17692110.16053994X-RAY DIFFRACTION100
2.0859-2.15330.20262090.1653979X-RAY DIFFRACTION99
2.1533-2.23020.18212120.16254023X-RAY DIFFRACTION100
2.2302-2.31950.19352100.17473981X-RAY DIFFRACTION100
2.3195-2.42510.19872110.17454021X-RAY DIFFRACTION100
2.4251-2.55290.19282130.17724040X-RAY DIFFRACTION100
2.5529-2.71290.19432100.18483987X-RAY DIFFRACTION100
2.7129-2.92230.17872130.17754048X-RAY DIFFRACTION100
2.9223-3.21630.18182130.1744056X-RAY DIFFRACTION100
3.2163-3.68160.18252150.16814085X-RAY DIFFRACTION100
3.6816-4.63790.17232170.15744129X-RAY DIFFRACTION100
4.6379-49.02920.19182270.18284287X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 109.5387 Å / Origin y: 6.8652 Å / Origin z: 158.5918 Å
111213212223313233
T0.1308 Å20.0029 Å20.0093 Å2-0.1285 Å20.0025 Å2--0.151 Å2
L0.2035 °20.0805 °20.0439 °2-0.5081 °20.0784 °2--0.2846 °2
S0.004 Å °0.0164 Å °0.0032 Å °-0.0038 Å °0.0087 Å °-0.0339 Å °0.0068 Å °0.0265 Å °-0.013 Å °
Refinement TLS groupSelection details: all

+
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