[English] 日本語
Yorodumi
- PDB-4hx3: Crystal structure of Streptomyces caespitosus sermetstatin in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hx3
TitleCrystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin
Components
  • Extracellular small neutral protease
  • Neutral proteinase inhibitor ScNPI
KeywordsHydrolase/Hydrolase Inhibitor / Streptomyces subtilisin inhibitor fold / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


snapalysin / serine-type endopeptidase inhibitor activity / metalloendopeptidase activity / proteolysis / extracellular region / zinc ion binding / metal ion binding
Similarity search - Function
Peptidase M7, snapalysin / Streptomyces extracellular neutral proteinase (M7) family / Subtilisin Inhibitor / Subtilisin inhibitor-like / Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor / Subtilisin inhibitor / Subtilisin inhibitor-like superfamily / Subtilisin inhibitor-like / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) ...Peptidase M7, snapalysin / Streptomyces extracellular neutral proteinase (M7) family / Subtilisin Inhibitor / Subtilisin inhibitor-like / Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor / Subtilisin inhibitor / Subtilisin inhibitor-like superfamily / Subtilisin inhibitor-like / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Extracellular small neutral protease / Neutral proteinase inhibitor ScNPI
Similarity search - Component
Biological speciesStreptomyces caespitosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTrillo-Muyo, S. / Martinez-Rodriguez, S. / Arolas, J.L. / Gomis-Ruth, F.X.
CitationJournal: CHEM SCI / Year: 2013
Title: Mechanism of action of a Janus-faced single-domain protein inhibitor simultaneously targeting two peptidase classes
Authors: Trillo-Muyo, S. / Martinez-Rodriguez, S. / Arolas, J.L. / Gomis-Ruth, F.X.
History
DepositionNov 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Feb 27, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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 / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Extracellular small neutral protease
B: Neutral proteinase inhibitor ScNPI
C: Extracellular small neutral protease
D: Neutral proteinase inhibitor ScNPI
E: Extracellular small neutral protease
F: Neutral proteinase inhibitor ScNPI
G: Extracellular small neutral protease
H: Neutral proteinase inhibitor ScNPI
I: Extracellular small neutral protease
J: Neutral proteinase inhibitor ScNPI
K: Extracellular small neutral protease
L: Neutral proteinase inhibitor ScNPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,54620
Polymers158,97012
Non-polymers5778
Water4,954275
1
A: Extracellular small neutral protease
B: Neutral proteinase inhibitor ScNPI
C: Extracellular small neutral protease
D: Neutral proteinase inhibitor ScNPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2137
Polymers52,9904
Non-polymers2233
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-94 kcal/mol
Surface area20600 Å2
MethodPISA
2
E: Extracellular small neutral protease
F: Neutral proteinase inhibitor ScNPI
G: Extracellular small neutral protease
H: Neutral proteinase inhibitor ScNPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1216
Polymers52,9904
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-96 kcal/mol
Surface area20400 Å2
MethodPISA
3
I: Extracellular small neutral protease
J: Neutral proteinase inhibitor ScNPI
K: Extracellular small neutral protease
L: Neutral proteinase inhibitor ScNPI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2137
Polymers52,9904
Non-polymers2233
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-95 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.540, 121.810, 130.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsdimer of dimer

-
Components

#1: Protein
Extracellular small neutral protease / SCNP / Snapalysin


Mass: 14571.586 Da / Num. of mol.: 6 / Fragment: Mature protease
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces caespitosus (bacteria) / Gene: snpA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56406, snapalysin
#2: Protein
Neutral proteinase inhibitor ScNPI / Sermetstatin


Mass: 11923.354 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces caespitosus (bacteria) / Gene: ScNPI / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: Q9FDS0
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 0.2 M magnesium chloride, 15.0% (v/v) ethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2012
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.7→89.1 Å / Num. all: 51602 / Num. obs: 51602 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 65.19 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.7

-
Processing

Software
NameVersionClassification
ProDCdata collection
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KUH,4HWX

1kuh

4hwx


Resolution: 2.7→43.49 Å / Cor.coef. Fo:Fc: 0.9239 / Cor.coef. Fo:Fc free: 0.8976 / SU R Cruickshank DPI: 0.714 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 782 1.52 %RANDOM
Rwork0.195 ---
all0.195 51602 --
obs0.1957 51481 99.54 %-
Displacement parametersBiso mean: 57.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.4897 Å20 Å20 Å2
2---2.9934 Å20 Å2
3---4.4831 Å2
Refine analyzeLuzzati coordinate error obs: 0.424 Å
Refinement stepCycle: LAST / Resolution: 2.7→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11041 0 18 275 11334
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111352HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0615533HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4929SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes316HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1697HARMONIC5
X-RAY DIFFRACTIONt_it11352HARMONIC20
X-RAY DIFFRACTIONt_nbd15SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion2.91
X-RAY DIFFRACTIONt_chiral_improper_torsion1468SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact12282SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2281 53 1.45 %
Rwork0.2263 3606 -
all0.2263 3659 -
obs--99.54 %
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)
11.3478-1.01651.23374.00540.92312.6585-0.05050.00650.137-0.0872-0.0515-0.3117-0.05720.32090.102-0.250.06280.0022-0.06790.0645-0.0036-23.7493-22.864224.2405
22.9744-0.02562.05383.24190.48644.1236-0.0110.23480.2318-0.6751-0.18270.3246-0.145-0.11020.1937-0.13350.1418-0.0766-0.0256-0.03360.045-48.0685-14.505710.1944
35.907-1.141-1.66487.4451.16624.78010.3792-0.00850.0748-0.1172-0.42390.83140.0341-0.69630.0447-0.24140.00340.04530.1398-0.10370.1294-70.6539-9.182931.4433
44.40090.94-0.59064.35410.98953.66980.2717-0.30170.7598-0.0270.0045-0.2457-0.64560.0405-0.2762-0.17960.0070.075-0.1503-0.04860.2346-43.68871.409426.6127
52.94390.9744-0.64937.9224-1.39645.1480.2222-0.5803-0.2335-0.1036-0.1962-1.62710.24680.9132-0.0259-0.15050.0314-0.04170.1414-0.00970.3922-5.2176-61.286717.4313
66.28062.84232.05425.0951.7713.66550.13530.12-0.62670.0336-0.0187-0.28150.34520.1775-0.1166-0.13530.05560.0151-0.1229-0.04940.037-30.3893-68.74093.5658
72.38790.2012-0.1056.05161.52044.257-0.1194-0.02790.0817-0.0725-0.31750.76250.0862-0.62380.4369-0.22840.06310.0208-0.0287-0.12020.0938-50.451-45.31146.8144
83.79211.9986-0.73964.16391.16942.2756-0.10250.45280.0313-0.67640.3226-0.3838-0.48840.1071-0.2201-0.0937-0.0040.1585-0.0379-0.03730.0511-23.8264-47.4263-3.6698
93.3211-0.78150.35161.5297-0.1944.0768-0.0282-0.0694-0.02690.18280.06420.10880.0301-0.3435-0.036-0.29240.05440.0107-0.10050.12880.0738-16.5261-40.785541.5487
104.3734-2.3132-0.76763.9104-0.26812.85050.1330.4473-0.0386-0.2966-0.0314-0.17680.3503-0.0867-0.1016-0.19870.0349-0.0389-0.1305-0.00270.19749.6321-53.711840.0417
113.43530.8591-0.64748.0101-0.07575.35740.0849-0.4257-0.36110.3999-0.8153-2.0587-0.42370.77520.7304-0.4647-0.1844-0.3032-0.27670.36370.829831.013-37.979156.4571
122.87030.8991-1.4432.8973-1.38893.73570.1085-0.3181-0.06450.4759-0.1144-0.4973-0.1684-0.02920.006-0.1729-0.0288-0.1584-0.120.02910.13824.8645-48.876463.0435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 132
2X-RAY DIFFRACTION1A201 - 999
3X-RAY DIFFRACTION2B1 - 113
4X-RAY DIFFRACTION3C-2 - 132
5X-RAY DIFFRACTION3C201 - 999
6X-RAY DIFFRACTION4D1 - 62
7X-RAY DIFFRACTION4D67 - 113
8X-RAY DIFFRACTION5E1 - 132
9X-RAY DIFFRACTION5E201 - 999
10X-RAY DIFFRACTION6F2 - 113
11X-RAY DIFFRACTION7G-1 - 132
12X-RAY DIFFRACTION7G201 - 999
13X-RAY DIFFRACTION8H-1 - 60
14X-RAY DIFFRACTION8H67 - 113
15X-RAY DIFFRACTION9I-2 - 132
16X-RAY DIFFRACTION9I201 - 999
17X-RAY DIFFRACTION10J1 - 65
18X-RAY DIFFRACTION10J68 - 113
19X-RAY DIFFRACTION11K-1 - 132
20X-RAY DIFFRACTION11K201 - 999
21X-RAY DIFFRACTION12L1 - 113

+
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