[English] 日本語
Yorodumi
- PDB-4ybf: Aspartic Proteinase Sapp2 Secreted from Candida Parapsilosis at 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ybf
TitleAspartic Proteinase Sapp2 Secreted from Candida Parapsilosis at 1.25 A Resolution
ComponentsCandidapepsin-2
KeywordsHYDROLASE / Aspartic Proteinase Sapp2
Function / homology
Function and homology information


candidapepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Secreted aspartic endopeptidase / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Secreted aspartic endopeptidase / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / candidapepsin
Similarity search - Component
Biological speciesCandida parapsilosis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsDostal, J. / Hruskova-Heidingsfeldova, O. / Rezacova, P. / Brynda, J. / Mareckova, L. / Pichova, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis.
Authors: Dostal, J. / Pecina, A. / Hruskova-Heidingsfeldova, O. / Mareckova, L. / Pichova, I. / Rezacova, P. / Lepsik, M. / Brynda, J.
History
DepositionFeb 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Candidapepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5802
Polymers35,4741
Non-polymers1061
Water4,143230
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint4 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.138, 57.147, 54.553
Angle α, β, γ (deg.)90.000, 90.610, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Candidapepsin-2


Mass: 35474.008 Da / Num. of mol.: 1 / Fragment: residues 72-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (strain CDC 317 / ATCC MYA-4646) (yeast)
Gene: CPAR2_102580 / Production host: Candida parapsilosis (yeast) / References: UniProt: G8B6Y8
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.915 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. all: 554808 / Num. obs: 84475 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 19.433 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.068 / Χ2: 0.968 / Net I/σ(I): 14.85 / Num. measured all: 554808
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.24-1.316.20.8860.5213.48239313813131930.56995.5
1.31-1.40.9590.335.398665713039127560.35797.8
1.4-1.520.9820.2057.937869112122119170.22398.3
1.52-1.660.9920.12512.367516811147110180.13598.8
1.66-1.860.9950.08517.66777810103100420.09399.4
1.86-2.140.9970.06324.4258383896388780.06899.1
2.14-2.620.9970.05728.6148164757875220.06299.3
2.62-3.70.9970.05132.3837232588258490.05699.4
3.70.9970.0533.8820342332933000.05499.1

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FV3

3fv3


Resolution: 1.24→39.46 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.243 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1745 4224 5 %RANDOM
Rwork0.1468 ---
obs0.1482 80251 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 108.89 Å2 / Biso mean: 15.833 Å2 / Biso min: 8.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0.02 Å2
2--0.76 Å20 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 1.24→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 7 233 2731
Biso mean--42.75 24.92 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022702
X-RAY DIFFRACTIONr_bond_other_d0.0010.021768
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9593724
X-RAY DIFFRACTIONr_angle_other_deg0.9743.0024375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2585380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.00225.739115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63315417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.887157
X-RAY DIFFRACTIONr_chiral_restr0.1080.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213149
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02527
X-RAY DIFFRACTIONr_rigid_bond_restr8.27934470
X-RAY DIFFRACTIONr_sphericity_free17.486558
X-RAY DIFFRACTIONr_sphericity_bonded7.79254562
LS refinement shellResolution: 1.238→1.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 295 -
Rwork0.176 5590 -
all-5885 -
obs--94.43 %

+
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