[English] 日本語
Yorodumi
- PDB-3h7o: Crystal structure of scabies mite inactivated protease paralogue ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h7o
TitleCrystal structure of scabies mite inactivated protease paralogue S-I1 (SMIPP-S-I1)
ComponentsGroup 3 allergen SMIPP-S Yv6023A04
KeywordsHYDROLASE
Function / homology
Function and homology information


serine-type endopeptidase activity
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold ...Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Group 3 allergen SMIPP-S Yv6023A04
Similarity search - Component
Biological speciesSarcoptes scabiei type hominis (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsBuckle, A.M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural mechanisms of inactivation in scabies mite serine protease paralogues.
Authors: Fischer, K. / Langendorf, C.G. / Irving, J.A. / Reynolds, S. / Willis, C. / Beckham, S. / Law, R.H. / Yang, S. / Bashtannyk-Puhalovich, T.A. / McGowan, S. / Whisstock, J.C. / Pike, R.N. / ...Authors: Fischer, K. / Langendorf, C.G. / Irving, J.A. / Reynolds, S. / Willis, C. / Beckham, S. / Law, R.H. / Yang, S. / Bashtannyk-Puhalovich, T.A. / McGowan, S. / Whisstock, J.C. / Pike, R.N. / Kemp, D.J. / Buckle, A.M.
History
DepositionApr 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Group 3 allergen SMIPP-S Yv6023A04
B: Group 3 allergen SMIPP-S Yv6023A04
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,28010
Polymers50,5272
Non-polymers7538
Water5,819323
1
A: Group 3 allergen SMIPP-S Yv6023A04
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7326
Polymers25,2641
Non-polymers4685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Group 3 allergen SMIPP-S Yv6023A04
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5484
Polymers25,2641
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.415, 80.578, 114.693
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Group 3 allergen SMIPP-S Yv6023A04 / Scabies Mite Inactivated Protease Paralogue S-I1 / SMIPP-S-I1


Mass: 25263.623 Da / Num. of mol.: 2 / Fragment: UNP residues 29-256 / Mutation: N111Q, N174Q, N218Q
Source method: isolated from a genetically manipulated source
Details: Expression and purification as described in Sun, J. et al. (1999) Expression and purification of recombinant human granzyme B from Pichia pastoris. Biochem Biophys Res Commun 261:251-255.
Source: (gene. exp.) Sarcoptes scabiei type hominis (arthropod)
Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: Q6VPT6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% v/v PEG 8000, 10% v/v Glycerol, 0.1 M Tris-HCl pH 8.5, 0.2 M Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Av σ(I) over netI: 7.1 / Number: 139304 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / D res high: 1.85 Å / D res low: 65.938 Å / Num. obs: 34997 / % possible obs: 91.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.8557.3591.910.0550.0554.1
4.145.8594.510.0520.0524.4
3.384.1495.610.0490.0494.4
2.933.3896.410.0540.0544.4
2.622.9397.410.0690.0694.4
2.392.6297.810.0930.0934.4
2.212.3998.310.1210.1214.3
2.072.2198.410.160.164.2
1.952.0785.710.2020.2023.2
1.851.9572.210.3240.3242.5
ReflectionResolution: 1.85→57.35 Å / Num. obs: 34997 / % possible obs: 91.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 7.115
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.952.50.3242.3992639700.32472.2
1.95-2.073.20.2023.71444444710.20285.7
2.07-2.214.20.164.42013247870.1698.4
2.21-2.394.30.1215.91958145240.12198.3
2.39-2.624.40.0937.81786940950.09397.8
2.62-2.934.40.069101634037380.06997.4
2.93-3.384.40.05411.31448232850.05496.4
3.38-4.144.40.04911.71213127590.04995.6
4.14-5.854.40.05211947021600.05294.5
5.85-57.354.10.0559.8492912080.05591.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.77 Å
Translation2.5 Å46.77 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.17data scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FI8

1fi8


Resolution: 1.85→57.35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.858 / SU B: 7.254 / SU ML: 0.097 / SU R Cruickshank DPI: 0.167 / SU Rfree: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1747 5 %RANDOM
Rwork0.186 ---
obs0.187 34954 91.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 74.73 Å2 / Biso mean: 31.866 Å2 / Biso min: 18.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--1.18 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.85→57.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 44 323 3853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223609
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.9824913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8335450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7925144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66515583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6821512
X-RAY DIFFRACTIONr_chiral_restr0.0660.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212692
X-RAY DIFFRACTIONr_mcbond_it0.76432258
X-RAY DIFFRACTIONr_mcangle_it1.47953667
X-RAY DIFFRACTIONr_scbond_it2.33871351
X-RAY DIFFRACTIONr_scangle_it3.676101246
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 103 -
Rwork0.254 1841 -
all-1944 -
obs--69.5 %
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)
12.5937-0.2083-1.02640.78090.20492.04570.0617-0.0945-0.0054-0.0336-0.03260.0005-0.031-0.0849-0.0291-0.125-0.0005-0.017-0.1589-0.003-0.141732.8553.57421.732
21.5645-0.4270.55650.9594-0.35432.47710.01960.0157-0.1244-0.00610.01190.10710.1523-0.142-0.0316-0.1335-0.00340.0112-0.17580.0024-0.118116.94145.14655.013
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 229
2X-RAY DIFFRACTION2B4 - 229

+
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