[English] 日本語
Yorodumi
- PDB-5p6l: Automated refinement of diffraction data obtained from an endothi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5p6l
TitleAutomated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 282
Componentsendothiapepsin
KeywordsHYDROLASE / fragment screening / method development / aspartic protease
Function / homology
Function and homology information


endothiapepsin / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Aspergillopepsin-like catalytic domain / 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 ...Aspergillopepsin-like catalytic domain / 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
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.049 Å
Model detailsAll 364 structures of this series were generated by an automated refinement pipeline and, thus, not ...All 364 structures of this series were generated by an automated refinement pipeline and, thus, not refined to full convergence (e.g. since no manual (re-)building was performed, fragments are missing in the structural model even when present as indicated by the electron density)
AuthorsSchiebel, J. / Heine, A. / Klebe, G.
CitationJournal: Structure / Year: 2016
Title: High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits.
Authors: Schiebel, J. / Krimmer, S.G. / Rower, K. / Knorlein, A. / Wang, X. / Park, A.Y. / Stieler, M. / Ehrmann, F.R. / Fu, K. / Radeva, N. / Krug, M. / Huschmann, F.U. / Glockner, S. / Weiss, M.S. ...Authors: Schiebel, J. / Krimmer, S.G. / Rower, K. / Knorlein, A. / Wang, X. / Park, A.Y. / Stieler, M. / Ehrmann, F.R. / Fu, K. / Radeva, N. / Krug, M. / Huschmann, F.U. / Glockner, S. / Weiss, M.S. / Mueller, U. / Klebe, G. / Heine, A.
History
DepositionJun 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.4Nov 17, 2021Group: Data collection / Database references / Structure summary
Category: database_2 / diffrn_radiation_wavelength / pdbx_deposit_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: endothiapepsin


Theoretical massNumber of molelcules
Total (without water)33,8141
Polymers33,8141
Non-polymers00
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.336, 73.084, 52.746
Angle α, β, γ (deg.)90.000, 109.350, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein endothiapepsin


Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystal obtained by streak-seeding and soaked with 90 mM of fragment 282 with the SMILES code C[C@@H]1CNC2=C(C=CC=C2C1)S(N)(=O)=O

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.05→41.135 Å / Num. obs: 148073 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.561 % / Biso Wilson estimate: 9.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.043 / Χ2: 0.988 / Net I/σ(I): 18.06 / Num. measured all: 527435
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.05-1.110.4952.216535724429214580.7570.59787.8
1.11-1.190.294.357945522974228720.9040.34399.6
1.19-1.280.2016.377787021389213390.9530.23699.8
1.28-1.410.1349.336994519705196400.9790.15899.7
1.41-1.570.07716.166761017808177720.9930.0999.8
1.57-1.820.04526.035768315754157150.9970.05299.8
1.82-2.220.02643.345072213314132680.9990.03199.7
2.22-3.140.02154.483770710334102770.9990.02499.4
3.140.01865.7421085579357310.9990.02198.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å39.56 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata scaling
PHENIXrefinement
PHASER2.5.7phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y5L

4y5l


Resolution: 1.049→39.56 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 11.87 / Stereochemistry target values: ML
Details: All 364 structures of this series were generated by an automated refinement pipeline and, thus, not refined to full convergence (e.g. since no manual (re-)building was performed, fragments ...Details: All 364 structures of this series were generated by an automated refinement pipeline and, thus, not refined to full convergence (e.g. since no manual (re-)building was performed, fragments are missing in the structural model even when present as indicated by the electron density)
RfactorNum. reflection% reflectionSelection details
Rfree0.1399 7404 5 %RANDOM
Rwork0.1262 140667 --
obs0.1269 148071 97.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.29 Å2 / Biso mean: 13.0242 Å2 / Biso min: 6.54 Å2
Refinement stepCycle: final / Resolution: 1.049→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 0 250 2619
Biso mean---24.85 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062426
X-RAY DIFFRACTIONf_angle_d1.2113329
X-RAY DIFFRACTIONf_chiral_restr0.072399
X-RAY DIFFRACTIONf_plane_restr0.006424
X-RAY DIFFRACTIONf_dihedral_angle_d10.717783
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0487-1.06060.25931740.25323303347769
1.0606-1.0730.23412050.24163898410381
1.073-1.08610.24522290.21424348457792
1.0861-1.09990.21742540.196348255079100
1.0999-1.11440.18722470.17094705495299
1.1144-1.12960.16672510.15644761501299
1.1296-1.14580.16162510.145347665017100
1.1458-1.16290.16542520.144247915043100
1.1629-1.1810.14512480.133347234971100
1.181-1.20040.14222520.123747685020100
1.2004-1.22110.13462510.116947805031100
1.2211-1.24330.11882490.112347354984100
1.2433-1.26720.13542550.111948325087100
1.2672-1.29310.12172510.110947685019100
1.2931-1.32120.12092510.106647815032100
1.3212-1.35190.12972510.105747615012100
1.3519-1.38580.1292510.102847805031100
1.3858-1.42320.11282510.101547725023100
1.4232-1.46510.1262520.096447855037100
1.4651-1.51240.11072530.093848035056100
1.5124-1.56650.10442510.093347615012100
1.5665-1.62920.11482520.094648015053100
1.6292-1.70330.12272510.101447615012100
1.7033-1.79310.12212520.102347945046100
1.7931-1.90550.11772530.106147915044100
1.9055-2.05260.11692530.106648165069100
2.0526-2.25910.12772520.10747815033100
2.2591-2.5860.14512530.12614805505899
2.586-3.25780.14522520.137348025054100
3.2578-39.58770.16742570.16384870512799

+
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