[English] 日本語
Yorodumi
- PDB-3rfi: Crystal structure of the saposin-like domain of plant aspartic pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rfi
TitleCrystal structure of the saposin-like domain of plant aspartic protease from Solanum tuberosum
ComponentsAsp
KeywordsHYDROLASE / Aspartic protease / PSI / Saposin
Function / homology
Function and homology information


lipid metabolic process / protein processing / aspartic-type endopeptidase activity
Similarity search - Function
Phytepsin / Saposin-like / NK-Lysin / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin B type domain / Saposin-like / Saposin B type domain profile. ...Phytepsin / Saposin-like / NK-Lysin / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin B type domain / Saposin-like / Saposin B type domain profile. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBhaumik, P. / Wlodawer, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and Mechanism of the Saposin-like Domain of a Plant Aspartic Protease.
Authors: Bryksa, B.C. / Bhaumik, P. / Magracheva, E. / De Moura, D.C. / Kurylowicz, M. / Zdanov, A. / Dutcher, J.R. / Wlodawer, A. / Yada, R.Y.
History
DepositionApr 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Aug 24, 2011Group: Database references
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Asp


Theoretical massNumber of molelcules
Total (without water)11,7801
Polymers11,7801
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Asp

A: Asp


Theoretical massNumber of molelcules
Total (without water)23,5592
Polymers23,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3490 Å2
ΔGint-43 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.470, 56.470, 55.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-153-

HOH

-
Components

#1: Protein Asp


Mass: 11779.507 Da / Num. of mol.: 1 / Fragment: StAP_PSI (UNP Residues 301-403)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Plasmid: pET32b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3)pLysS / References: UniProt: Q6B9W9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium sulfate monohydrate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 8363 / Num. obs: 8355 / % possible obs: 99.9 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 24.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.87 / Num. unique all: 1159 / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.179 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 417 5 %RANDOM
Rwork0.18697 ---
obs0.18995 7936 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms620 0 0 63 683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022645
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.978873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.703580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.42327.30826
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08415128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg34.286151
X-RAY DIFFRACTIONr_chiral_restr0.1460.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021460
X-RAY DIFFRACTIONr_mcbond_it1.0491.5401
X-RAY DIFFRACTIONr_mcangle_it1.9832653
X-RAY DIFFRACTIONr_scbond_it3.8073244
X-RAY DIFFRACTIONr_scangle_it6.2984.5219
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 30 -
Rwork0.342 573 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.6669-2.33372.486.6758-0.51944.93680.0406-0.122-0.18840.04190.0140.15020.3919-0.0247-0.05460.1165-0.0414-0.02570.1940.0270.077921.53217.1377.673
22.36370.2094-0.54546.4362-4.89176.64840.0093-0.05190.21650.2657-0.0611-0.0592-0.54630.08290.05190.1224-0.0047-0.02880.1047-0.02840.07545.19632.676-2.875
313.2676-6.6944-3.62877.40461.59434.6212-0.1935-0.3067-0.72080.38810.13060.46530.4765-0.05160.06290.2093-0.02670.00350.12710.03510.165916.9029.2532.977
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 26
2X-RAY DIFFRACTION2A27 - 82
3X-RAY DIFFRACTION3A83 - 103

+
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