[English] 日本語
Yorodumi
- PDB-3k50: Crystal structure of Putative S41 protease (YP_211611.1) from Bac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k50
TitleCrystal structure of Putative S41 protease (YP_211611.1) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution
ComponentsPutative S41 protease
KeywordsHYDROLASE / Putative S41 protease / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / UNKNOWN FUNCTION
Function / homology
Function and homology information


serine-type peptidase activity / proteolysis
Similarity search - Function
Transcription Regulator spoIIAA - #170 / Peptidase S41, N-terminal / Peptidase S41 N-terminal domain / Tail specific protease / Peptidase family S41 / Transcription Regulator spoIIAA / PDZ domain 6 / PDZ domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 ...Transcription Regulator spoIIAA - #170 / Peptidase S41, N-terminal / Peptidase S41 N-terminal domain / Tail specific protease / Peptidase family S41 / Transcription Regulator spoIIAA / PDZ domain 6 / PDZ domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / PDZ domain / Pdz3 Domain / ClpP/crotonase-like domain superfamily / PDZ domain profile. / PDZ domain / PDZ superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Peptidase S41 / Peptidase S41
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative S41 protease (YP_211611.1) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: 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 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative S41 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0494
Polymers45,8301
Non-polymers2203
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.274, 91.435, 107.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Putative S41 protease


Mass: 45829.508 Da / Num. of mol.: 1 / Fragment: sequence database residues 24-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Strain: ATCC 25285 / NCTC 9343 / Gene: BF1979 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LDX8, UniProt: A0A380YY03*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 24-425 OF THE FULL LENGTH PROTEIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.0000M LiCl, 20.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979361
ReflectionResolution: 2→29.311 Å / Num. obs: 28549 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.59 % / Biso Wilson estimate: 25.478 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 9.72
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.5481.590404751189.6
2.07-2.150.416299775204199
2.15-2.250.3062.6105765507198.9
2.25-2.370.2463.4105305475199
2.37-2.520.1834.4104435429199.2
2.52-2.710.155.5101505253199
2.71-2.990.0978.1106805517199.3
2.99-3.420.05314.1103715346199.3
3.42-4.30.02824.3104175367198.9
4.3-29.310.02230.6104255321197.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.311 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 7.462 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.149
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.CHLORIDE ION AND GLYCEROL MOLECULES FROM CRYSTALLIZATION AND CRYOPROTECTANT ARE MODELED IN THE STRUCTURE, RESPECTIVELY.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1442 5.1 %RANDOM
Rwork0.157 ---
obs0.159 28503 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 83.75 Å2 / Biso mean: 37.277 Å2 / Biso min: 17.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---1.86 Å20 Å2
3---1.94 Å2
Refinement stepCycle: LAST / Resolution: 2→29.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3035 0 13 317 3365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223198
X-RAY DIFFRACTIONr_bond_other_d0.0020.022109
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.9664363
X-RAY DIFFRACTIONr_angle_other_deg1.0835153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8645402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47924.437142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26415506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9811515
X-RAY DIFFRACTIONr_chiral_restr0.0920.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023605
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02649
X-RAY DIFFRACTIONr_nbd_refined0.2260.3592
X-RAY DIFFRACTIONr_nbd_other0.1840.32170
X-RAY DIFFRACTIONr_nbtor_refined0.1860.51546
X-RAY DIFFRACTIONr_nbtor_other0.090.51591
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.5372
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.363
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.526
X-RAY DIFFRACTIONr_mcbond_it2.39732051
X-RAY DIFFRACTIONr_mcbond_other0.6843798
X-RAY DIFFRACTIONr_mcangle_it3.2653222
X-RAY DIFFRACTIONr_scbond_it5.28881343
X-RAY DIFFRACTIONr_scangle_it6.987111141
LS refinement shellResolution: 2.005→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 104 -
Rwork0.209 1922 -
all-2026 -
obs--97.26 %
Refinement TLS params.Method: refined / Origin x: 4.8455 Å / Origin y: 25.6464 Å / Origin z: 20.3174 Å
111213212223313233
T-0.0437 Å20.0097 Å2-0.0115 Å2--0.02 Å2-0.0083 Å2---0.0523 Å2
L0.3767 °20.004 °2-0.2258 °2-0.7538 °2-0.2305 °2--0.7767 °2
S0.0005 Å °-0.0653 Å °0.0412 Å °0.1397 Å °0.0195 Å °0.0149 Å °-0.1197 Å °-0.0033 Å °-0.02 Å °

+
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