[English] 日本語
Yorodumi
- PDB-3i6s: Crystal Structure of the plant subtilisin-like protease SBT3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i6s
TitleCrystal Structure of the plant subtilisin-like protease SBT3
ComponentsSubtilisin-like protease
KeywordsHYDROLASE / subtilisin-like / protease / PA-domain / FN3-domain
Function / homology
Function and homology information


regulation of cell wall pectin metabolic process / plant-type cell wall modification / positive regulation of defense response to insect / self proteolysis / peptide catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / defense response / response to wounding / serine-type endopeptidase activity ...regulation of cell wall pectin metabolic process / plant-type cell wall modification / positive regulation of defense response to insect / self proteolysis / peptide catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / defense response / response to wounding / serine-type endopeptidase activity / positive regulation of gene expression / protein homodimerization activity / proteolysis / extracellular space / identical protein binding
Similarity search - Function
Immunoglobulin-like - #2310 / Cucumisin-like catalytic domain / Subtilisin-like protease, fibronectin type-III domain / Subtilisin-like protease / Fibronectin type-III domain / Glucose Oxidase; domain 1 - #30 / Glucose Oxidase; domain 1 / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily ...Immunoglobulin-like - #2310 / Cucumisin-like catalytic domain / Subtilisin-like protease, fibronectin type-III domain / Subtilisin-like protease / Fibronectin type-III domain / Glucose Oxidase; domain 1 - #30 / Glucose Oxidase; domain 1 / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family / 3-Layer(bba) Sandwich / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Subtilisin-like protease SBT3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 Å
AuthorsRose, R. / Ottmann, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural basis for Ca2+-independence and activation by homodimerization of tomato subtilase 3.
Authors: Ottmann, C. / Rose, R. / Huttenlocher, F. / Cedzich, A. / Hauske, P. / Kaiser, M. / Huber, R. / Schaller, A.
History
DepositionJul 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / 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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)142,3698
Polymers139,2952
Non-polymers3,0746
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint55 kcal/mol
Surface area49410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.890, 143.890, 195.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A113 - 761
2112B113 - 761

-
Components

#1: Protein Subtilisin-like protease


Mass: 69647.500 Da / Num. of mol.: 2 / Fragment: UNP residues 113-761 / Source method: isolated from a natural source / Details: cell culture / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: O82777
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 100 mM Bicine, 2.0 M NaCl, 10% (w/v) PEG 6000, 10 mM hexamminecobalt(III) chloride, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSLS X10SA11.5
SYNCHROTRONSLS X10SA21.008
ROTATING ANODERIGAKU31.541
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDJun 30, 2007
MARMOSAIC 225 mm CCD2CCDMay 25, 2008
MAR scanner 345 mm plate3IMAGE PLATEAug 13, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.51
21.0081
31.5411
ReflectionNumber: 1017085 / Rmerge(I) obs: 0.112 / D res high: 2.5 Å / Num. obs: 135037 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
152036899.710.045
1015148499.810.05
5101480799.910.063
451611310010.08
3.84549899.910.092
3.53.81077399.910.107
3.43.5450799.910.124
33.42444499.910.176
2.535704399.910.424
ReflectionResolution: 2.5→20 Å / Num. all: 135407 / Num. obs: 71081 / % possible obs: 99.7 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 12.13
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obs% possible all
2.5-30.4245.199.9
3-3.40.17611.399.9
3.4-3.50.12414.999.9
3.5-3.80.10716.799.9
3.8-40.09218.599.9
4-50.0820.9100
5-100.06322.999.9
10-150.0524.999.8
15-200.04524.899.7

-
Phasing

PhasingMethod: MIRAS
Phasing dmFOM : 0.73 / FOM acentric: 0.73 / FOM centric: 0.7 / Reflection: 25676 / Reflection acentric: 22551 / Reflection centric: 3125
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10-19.8980.890.90.86983735248
6.3-100.840.850.8134142861553
5-6.30.770.770.7343243766558
4.4-50.770.790.6943613860501
3.8-4.40.70.710.6477776972805
3.5-3.80.590.60.5248174357460
Phasing MIR der
IDDer set-ID
11
21
31
Phasing MIR der site
IDDer-IDBiso (Å)Atom type symbolFract xFract yFract zOccupancy
1160Cs0.51620.05480.0660.9622
1234.0941Cs0.26030.05320.05630.3096
1323.2865Cs0.31880.06620.04740.3968
2111.8249Hg0.22190.08710.11440.4994
2260Hg0.61320.14210.03610.4974
231Hg0.24930.08780.10720.0081

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVE2.09phasing
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→19.99 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28262 3554 5 %RANDOM
Rwork0.2486 ---
obs0.25032 67526 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: 50.096 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2---1.9 Å20 Å2
3---3.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9666 0 204 502 10372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210104
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.9813769
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4251269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.03224.148393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.118151564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1681552
X-RAY DIFFRACTIONr_chiral_restr0.090.21606
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217557
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4581.56377
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.864210295
X-RAY DIFFRACTIONr_scbond_it1.22433727
X-RAY DIFFRACTIONr_scangle_it2.0764.53474
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2552tight positional0.020.05
2261medium positional0.030.5
2552tight thermal0.320.5
2261medium thermal0.362
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 256 -
Rwork0.338 4864 -
obs--100 %

+
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