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- PDB-3i74: Crystal Structure of the plant subtilisin-like protease SBT3 in c... -

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Basic information

Entry
Database: PDB / ID: 3i74
TitleCrystal Structure of the plant subtilisin-like protease SBT3 in complex with a chloromethylketone inhibitor
Components
  • ACE-PHE-GLU-LYS-ALA chloromethylketone INHIBITOR
  • Subtilisin-like protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / subtilisin-like protease / PA-domain / FN3-domain / chloromethylketone inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / 3-Layer(bba) Sandwich / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACE-PHE-GLU-LYS-ALA chloromethylketone INHIBITOR / Subtilisin-like protease SBT3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Subtilisin-like protease
B: Subtilisin-like protease
C: ACE-PHE-GLU-LYS-ALA chloromethylketone INHIBITOR
D: ACE-PHE-GLU-LYS-ALA chloromethylketone INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,47910
Polymers140,4054
Non-polymers3,0746
Water7,873437
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.730, 143.730, 195.190
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
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A113 - 761
2114B113 - 761
1124A1 - 10
2124B1 - 10

NCS ensembles :
ID
1
2

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Components

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Protein / Protein/peptide / Non-polymers , 3 types, 441 molecules ABCD

#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: Protein/peptide ACE-PHE-GLU-LYS-ALA chloromethylketone INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 555.087 Da / Num. of mol.: 2 / Source method: obtained synthetically
References: ACE-PHE-GLU-LYS-ALA chloromethylketone INHIBITOR
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 6 molecules

#3: 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
#4: 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
#5: 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

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Details

Compound detailsTHE UNBOUND FORM OF THE INHIBITOR (CHAINS C,D) IS ACE-PHE-GLU-LYS-ALA CHLOROMETHYLKETONE. UPON ...THE UNBOUND FORM OF THE INHIBITOR (CHAINS C,D) IS ACE-PHE-GLU-LYS-ALA CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 538 FORMING A HEMIKETAL ALV AND 2) A COVALENT BOND TO NE2 OF HIS 215.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.75 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99994 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 63423 / Num. obs: 63093 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.49
Reflection shellResolution: 2.6→2.8 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 5.5 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.3 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å19.99 Å
Translation2.6 Å19.99 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.99 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.876 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.3 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.502 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29369 3155 5 %RANDOM
Rwork0.24964 ---
obs0.25181 59937 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: 40.016 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å20 Å2
2---1.72 Å20 Å2
3---3.45 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9750 0 204 437 10391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.02210187
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.5691.98113875
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.70951275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.2824.171398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.454151579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2161552
X-RAY DIFFRACTIONr_chiral_restr0.0380.21615
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0217615
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_it0.2141.56427
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.392210368
X-RAY DIFFRACTIONr_scbond_it0.32533760
X-RAY DIFFRACTIONr_scangle_it0.6084.53507
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
114821medium positional0.150.5
2238medium positional0.250.5
114821medium thermal0.082
2238medium thermal0.032
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 228 -
Rwork0.346 4325 -
obs--100 %

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