[English] 日本語
Yorodumi
- PDB-4tr2: Crystal structure of PvSUB1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tr2
TitleCrystal structure of PvSUB1
ComponentsSubtilisin-like 1 serine protease
KeywordsHYDROLASE / plasmodium egress protease / calcium-binding
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
SUB1 protease prodomain ProdP9 / SUB1 protease Prodomain ProdP9 / Subtilisin SUB1-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site ...SUB1 protease prodomain ProdP9 / SUB1 protease Prodomain ProdP9 / Subtilisin SUB1-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / subtilisin
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGiganti, D. / Bouillon, A. / Martinez, M. / Weber, P. / Girard-Blanc, C. / Petres, S. / Haouz, A. / Barale, J.C. / Alzari, P.M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-RPIB-002 France
CitationJournal: Nat Commun / Year: 2014
Title: A novel Plasmodium-specific prodomain fold regulates the malaria drug target SUB1 subtilase.
Authors: Giganti, D. / Bouillon, A. / Tawk, L. / Robert, F. / Martinez, M. / Crublet, E. / Weber, P. / Girard-Blanc, C. / Petres, S. / Haouz, A. / Hernandez, J.F. / Mercereau-Puijalon, O. / Alzari, P.M. / Barale, J.C.
History
DepositionJun 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Subtilisin-like 1 serine protease
B: Subtilisin-like 1 serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,87615
Polymers147,0812
Non-polymers79513
Water27015
1
A: Subtilisin-like 1 serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9868
Polymers73,5401
Non-polymers4457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Subtilisin-like 1 serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8917
Polymers73,5401
Non-polymers3506
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-87 kcal/mol
Surface area35950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.000, 95.000, 287.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Subtilisin-like 1 serine protease


Mass: 73540.398 Da / Num. of mol.: 2 / Fragment: Residues 26-630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: sub1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: E6Y8B9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M phosphate citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.7→45 Å / Num. obs: 37100 / % possible obs: 99.4 % / Redundancy: 8.6 % / Biso Wilson estimate: 60.13 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 9.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.6 / % possible all: 100

-
Processing

SoftwareName: BUSTER / Version: 2.11.4 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2TEC, 1DBI, 1CGI, 1R0R, 1LW6, 1EA7, and 1IC6

2tec

1dbi

1cgi

1r0r

1lw6

1ea7

1ic6


Resolution: 2.7→45.1 Å / Cor.coef. Fo:Fc: 0.9288 / Cor.coef. Fo:Fc free: 0.8957 / SU R Cruickshank DPI: 0.537 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.541 / SU Rfree Blow DPI: 0.29 / SU Rfree Cruickshank DPI: 0.294
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1853 4.99 %RANDOM
Rwork0.1999 ---
obs0.2021 37100 99.63 %-
Displacement parametersBiso mean: 61.98 Å2
Baniso -1Baniso -2Baniso -3
1--5.2931 Å20 Å20 Å2
2---5.2931 Å20 Å2
3---10.5861 Å2
Refine analyzeLuzzati coordinate error obs: 0.418 Å
Refinement stepCycle: 1 / Resolution: 2.7→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7362 0 33 15 7410
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097505HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1510166HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2653SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes229HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1069HARMONIC5
X-RAY DIFFRACTIONt_it7505HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion20.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion995SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8902SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2799 130 4.6 %
Rwork0.2208 2695 -
all0.2236 2825 -
obs--99.63 %
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)
10.18-0.05660.6440.0156-0.15642.19850.0866-0.0351-0.0358-0.0551-0.0819-0.03520.1392-0.0593-0.00470.07940.03360.0704-0.0276-0.0662-0.3228-4.0353-38.1373-17.3582
20.2772-0.1626-0.02830.3508-0.60242.67110.15030.32390.028-0.3218-0.1945-0.06580.50630.13080.04420.46380.04090.05770.57550.0401-0.09811.2971-48.632916.0393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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