[English] 日本語
Yorodumi
- PDB-2wv7: Intracellular subtilisin precursor from B. clausii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wv7
TitleIntracellular subtilisin precursor from B. clausii
ComponentsINTRACELLULAR SUBTILISIN PROTEASE
KeywordsHYDROLASE / INTRACELLULAR PROTEINASE REGULATION
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / identical protein binding / metal ion binding
Similarity search - Function
: / Subtilisin Carlsberg-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 / Peptidase S8, subtilisin-related ...: / Subtilisin Carlsberg-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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Intracellular subtilisin protease
Similarity search - Component
Biological speciesBACILLUS CLAUSII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsVevodova, J. / Gamble, M. / Ariza, A. / Dodson, E. / Jones, D.D. / Wilson, K.S.
CitationJournal: Structure / Year: 2010
Title: Crystal Structure of an Intracellular Subtilisin Reveals Novel Structural Features Unique to This Subtilisin Family.
Authors: Vevodova, J. / Gamble, M. / Kunze, G. / Ariza, A. / Dodson, E. / Jones, D.D. / Wilson, K.S.
History
DepositionOct 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INTRACELLULAR SUBTILISIN PROTEASE
B: INTRACELLULAR SUBTILISIN PROTEASE
C: INTRACELLULAR SUBTILISIN PROTEASE
D: INTRACELLULAR SUBTILISIN PROTEASE
E: INTRACELLULAR SUBTILISIN PROTEASE
F: INTRACELLULAR SUBTILISIN PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,77911
Polymers209,6646
Non-polymers1155
Water5,783321
1
A: INTRACELLULAR SUBTILISIN PROTEASE
B: INTRACELLULAR SUBTILISIN PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9113
Polymers69,8882
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-27.1 kcal/mol
Surface area20990 Å2
MethodPISA
2
C: INTRACELLULAR SUBTILISIN PROTEASE
D: INTRACELLULAR SUBTILISIN PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9344
Polymers69,8882
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-37.5 kcal/mol
Surface area21070 Å2
MethodPISA
3
E: INTRACELLULAR SUBTILISIN PROTEASE
F: INTRACELLULAR SUBTILISIN PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9344
Polymers69,8882
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-39.4 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.829, 119.829, 106.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A3 - 402
2114B3 - 402
3114C3 - 402
4114D3 - 402
5114E3 - 402
6114F3 - 402

NCS oper:
IDCodeMatrixVector
1given(-0.6384, 0.7692, -0.0278), (0.7697, 0.6383, -0.0101), (0.01, -0.0279, -0.9996)7.3848, -2.949, 65.1895
2given(0.7311, 0.6822, -0.003), (0.6822, -0.731, 0.0136), (0.0071, -0.012, -0.9999)57.2641, -41.6108, 31.1338
3given(0.013, 0.9996, -0.0251), (-0.9996, 0.0136, 0.0237), (0.0241, 0.0248, 0.9994)60.677, -34.4581, -34.069
4given(0.7282, -0.6828, 0.0587), (0.6852, 0.7273, -0.0405), (-0.0151, 0.0697, 0.9975)-68.9449, 33.2229, -4.0509
5given(-0.9944, 0.1021, -0.0263), (0.1024, 0.9947, -0.0093), (0.0252, -0.012, -0.9996)-59.4228, 34.4761, 60.4674

-
Components

#1: Protein
INTRACELLULAR SUBTILISIN PROTEASE


Mass: 34944.020 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CLAUSII (bacteria)
Description: ISOLATED FROM A NOVOZYMES STRAIN OF B. CLAUSII. STRAIN NUMBER AVAILABLE ON REQUEST.
Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: D0AB41, subtilisin
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M BISTRIS PH 6.5, 0.1M NACL, 1.5M AMMONIUM SULFATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.45→46.6 Å / Num. obs: 62796 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.6
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHASERphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YJC

1yjc


Resolution: 2.45→46.62 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.844 / SU B: 27.139 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 0.82 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3905 6.2 %RANDOM
Rwork0.197 ---
obs0.202 58858 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å21.26 Å20 Å2
2--2.52 Å20 Å2
3----3.78 Å2
Refinement stepCycle: LAST / Resolution: 2.45→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13168 0 5 321 13494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213418
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.95418186
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97851766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94424.746552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.752152076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3141567
X-RAY DIFFRACTIONr_chiral_restr0.1150.22105
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110145
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_it0.251.58787
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.435213974
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.80934631
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2454.54212
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2166 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.340.5
2Bmedium positional0.370.5
3Cmedium positional0.320.5
4Dmedium positional0.330.5
5Emedium positional0.370.5
6Fmedium positional0.390.5
1Amedium thermal1.922
2Bmedium thermal1.162
3Cmedium thermal1.952
4Dmedium thermal1.322
5Emedium thermal0.962
6Fmedium thermal1.522
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 315 -
Rwork0.276 4335 -
obs--99.79 %
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)
12.6113-0.5237-0.6051.68130.06421.4089-0.07310.0346-0.1342-0.013-0.0039-0.07720.15460.11060.0770.02060.01430.01020.01370.00750.197714.935-20.28928.497
22.4895-0.33990.29061.64520.38132.3479-0.0015-0.1922-0.06860.2221-0.08050.2130.2164-0.43630.0820.0616-0.02590.02960.1146-0.02080.246-17.317-5.98238.007
31.56080.1813-0.38361.8975-0.03861.19430.015-0.06250.04510.09670.0168-0.0152-0.05990.0467-0.03180.01910.02180.00380.05060.01650.187754.993-17.4683.098
41.88490.24850.29232.64580.44131.41210.0340.102-0.2891-0.081-0.03120.19350.2369-0.1407-0.00280.1148-0.01160.02060.101-0.00920.290741.094-49.887-5.432
53.18470.3252-0.23451.70980.10491.1058-0.00560.1813-0.0629-0.05480.0114-0.0526-0.00230.1018-0.00580.06620.0178-0.02140.07-0.00660.2649-44.23927.83222.841
63.61910.6786-0.3771.6495-0.2241.41660.0246-0.0182-0.40980.064-0.0060.1160.1455-0.1899-0.01860.0859-0.0033-0.02060.0973-0.00080.3589-77.57816.11332.572
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 402
2X-RAY DIFFRACTION2B3 - 402
3X-RAY DIFFRACTION3C3 - 402
4X-RAY DIFFRACTION4D3 - 402
5X-RAY DIFFRACTION5E3 - 402
6X-RAY DIFFRACTION6F3 - 402

+
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