[English] 日本語
Yorodumi
- PDB-9uf9: CRYSTAL STRUCTURE OF PEPSTATIN A BOUND TO RHODOTORULA MUCILAGINOS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9uf9
TitleCRYSTAL STRUCTURE OF PEPSTATIN A BOUND TO RHODOTORULA MUCILAGINOSA ASPARTIC PROTEASE RmuAP1
Components
  • Pepstatin A
  • Type I transmembrane sorting receptor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Pepstatin / Type I transmembrane sorting receptor
Similarity search - Component
Biological speciesRhodotorula mucilaginosa (fungus)
Streptomyces argenteolus subsp. toyonakensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsZhang, Y.-H. / Lin, C.-L. / Meng, M.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Molecular and crystal structure of RmuAP1-pepstatin A complex refined at 1.8 A resolution.
Authors: Zhang, Y.-H. / Lin, C.-L. / Meng, M.H.
History
DepositionApr 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
I: Pepstatin A
A: Type I transmembrane sorting receptor


Theoretical massNumber of molelcules
Total (without water)35,2962
Polymers35,2962
Non-polymers00
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.519, 52.833, 157.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-590-

HOH

21A-659-

HOH

-
Components

#1: Protein/peptide Pepstatin A


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 685.891 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Streptomyces argenteolus subsp. toyonakensis (bacteria)
References: Pepstatin
#2: Protein Type I transmembrane sorting receptor


Mass: 34609.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodotorula mucilaginosa (fungus) / Gene: PEP1_2, C6P46_002930 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A9P6W3R0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 50mM Sodium acetate (pH 5.0), 0.1M sodium phosphate monobasic monohydrate, 0.1M potassium phosphate monobasic, 0.1M MES monohydrate pH 6.5, 2.0M sodium chloride

-
Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97906 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 1.78→30 Å / Num. obs: 61645 / % possible obs: 95.8 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 8.69
Reflection shellResolution: 1.78→1.89 Å / Rmerge(I) obs: 0.388 / Num. unique obs: 9849

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→28.6 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 1699 5.01 %
Rwork0.1746 --
obs0.1762 33919 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 0 330 2782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062488
X-RAY DIFFRACTIONf_angle_d0.9473399
X-RAY DIFFRACTIONf_dihedral_angle_d8.002360
X-RAY DIFFRACTIONf_chiral_restr0.073390
X-RAY DIFFRACTIONf_plane_restr0.006436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.830.31241360.2322568X-RAY DIFFRACTION96
1.83-1.890.22611380.1942659X-RAY DIFFRACTION100
1.89-1.960.21671400.17892660X-RAY DIFFRACTION100
1.96-2.040.22531390.17232642X-RAY DIFFRACTION100
2.04-2.130.20571400.17872649X-RAY DIFFRACTION100
2.13-2.240.20941410.17052683X-RAY DIFFRACTION100
2.24-2.380.24241410.18432674X-RAY DIFFRACTION99
2.38-2.570.24221410.18392673X-RAY DIFFRACTION99
2.57-2.820.241430.19252711X-RAY DIFFRACTION100
2.82-3.230.19951440.18462719X-RAY DIFFRACTION100
3.23-4.070.18041460.1592761X-RAY DIFFRACTION100
4.07-28.60.14421500.14752821X-RAY DIFFRACTION97

+
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