[English] 日本語
Yorodumi
- PDB-5ard: Cooperative bio-metallic selectivity in a tailored protease enabl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ard
TitleCooperative bio-metallic selectivity in a tailored protease enables creation of a C-C cross-coupling Heckase
ComponentsSUBTILISIN SAVINASE
KeywordsHYDROLASE / PROTEASE / SUBTILISIN / CATALYSIS / PALLADIUM / METALLOENZYME / HECK REACTION / CROSS-COUPLING
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / serine-type endopeptidase activity / proteolysis / extracellular region / 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 / Serine proteases, subtilase domain profile. ...: / 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-methyl-2-(5-methylpyridin-2-yl)pyridine / NICKEL (II) ION / Subtilisin Savinase
Similarity search - Component
Biological speciesBACILLUS LENTUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSharma, M. / Diaz-Rodriguez, A. / Offen, W.A. / Palm-Espling, M.E. / Pordea, A. / Wormald, M.R. / Mcdonough, M. / Davies, G.J. / Davis, B.G.
CitationJournal: To be Published
Title: Cooperative Bio-Metallic Selectivity in a Tailored Protease Enables Creation of a C-C Cross-Coupling Heckase
Authors: Sharma, M. / Diaz-Rodriguez, A. / Offen, W.A. / Palm-Espling, M.E. / Pordea, A. / Wormald, M.R. / Mcdonough, M. / Davies, G.J. / Davis, B.G.
History
DepositionSep 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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.pdbx_leaving_atom_flag / _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: SUBTILISIN SAVINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2727
Polymers26,7081
Non-polymers5636
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.059, 61.280, 74.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein SUBTILISIN SAVINASE / ALKALINE PROTEASE / SUBTILISIN


Mass: 26708.365 Da / Num. of mol.: 1 / Fragment: MATURE PEPTIDE CHAIN, RESIDUES 1-269 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS LENTUS (bacteria) / Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: P29600, subtilisin

-
Non-polymers , 6 types, 232 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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: Chemical ChemComp-EI3 / 5-methyl-2-(5-methylpyridin-2-yl)pyridine


Mass: 184.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsSEQUENCE IS SAME FOR DEPOSITED COORDINATES, APART FROM LEU217 WHICH IS MUTATED TO CYS, BUT ...SEQUENCE IS SAME FOR DEPOSITED COORDINATES, APART FROM LEU217 WHICH IS MUTATED TO CYS, BUT NUMBERING IS NON- CONTIGUOUS AS IT IS BASED ON ALIGNMENT TO AN HOMOLOGOUS SECTION OF UNIPROT SEQUENCE P00782 FOR SUBTILISIN BPN' FROM BACILLUS AMYLOLIQUEFACIENS, RESIDUES 108 TO 382. THUS THERE ARE NO RESIDUES 36, 58, 158-159 OR 163-164.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 7.5
Details: 33% PEG 3350, 100 MM AMMONIUM SULFATE, 0.1 M TRIS PH 7.5

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.55→47.37 Å / Num. obs: 35362 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.4
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCI

1gci


Resolution: 1.55→47.37 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.299 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS COMPLETE ELECTRON DENSITY FOR THE RING OF THE BIPYRIDINE ADJACENT TO CYS217 AT A CONTOUR LEVEL OF 1 RMSD, AND FOR THE SECOND RING ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS COMPLETE ELECTRON DENSITY FOR THE RING OF THE BIPYRIDINE ADJACENT TO CYS217 AT A CONTOUR LEVEL OF 1 RMSD, AND FOR THE SECOND RING AT 0.7 RSMD, WITH THE BIPYRIDINE MODELLED AT AN OCCUPANCY OF 0.5. THERE IS ADDITIONAL PLANAR SHAPED DENSITY, WHICH HAS BEEN UNABLE TO BE MODELLED, BETWEEN CYS217 AND HIS64. THE NICKEL ION AND COORDINATED WATERS HAVE BEEN MODELLED AT AN OCCUPANCY OF 0.5. THERE ARE 2 REGIONS OF UNMODELLED DENSITY, BETWEEN THE SIDE CHAINS OF ASN155, PHE189 AND ASN218, AND BETWEEN THE SIDE CHAINS OF SER56, THR57 AND GLN59. THERE IS ONLY ONE CA ION, ALTHOUGH THE GENERAL ANNOTATION FOR UNIPROT ENTRY P29600 COMMENTS THAT 2 CALCIUM IONS BIND PER SUBUNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.15442 1805 5.1 %RANDOM
Rwork0.13492 ---
obs0.13594 33500 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.258 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å20 Å2
2---1.01 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.55→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 33 226 2137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192016
X-RAY DIFFRACTIONr_bond_other_d0.0020.021871
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9462754
X-RAY DIFFRACTIONr_angle_other_deg1.0634291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8235278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23624.7374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15915278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.511510
X-RAY DIFFRACTIONr_chiral_restr0.1150.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212405
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02461
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_it1.0841.1621106
X-RAY DIFFRACTIONr_mcbond_other1.0561.161105
X-RAY DIFFRACTIONr_mcangle_it1.6091.7381383
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7421.353910
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 131 -
Rwork0.193 2450 -
obs--100 %

+
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://pdbjlvh1.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