[English] 日本語
Yorodumi
- PDB-5njc: E. coli Microcin-processing metalloprotease TldD/E (TldD E263A mu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5njc
TitleE. coli Microcin-processing metalloprotease TldD/E (TldD E263A mutant) with hexapeptide bound
Components
  • (Metalloprotease ...) x 2
  • VAL-LEU-GLU-ASP-ARG-ILE
KeywordsHYDROLASE / metalloprotease / microcin / CcdA / DNA gyrase
Function / homology
Function and homology information


peptidase complex / Hydrolases; Acting on peptide bonds (peptidases) / protein processing / metallopeptidase activity / iron ion binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
TldD / : / PmbA/TldD fold / PmbA/TldD superfamily / Metalloprotease TldD/E, N-terminal domain / Metalloprotease TldD/PmbA, N-terminal / Metalloprotease TldD/PmbA superfamily / Metalloprotease TldD/E, C-terminal domain / Metalloprotease TldD/E, central domain / : ...TldD / : / PmbA/TldD fold / PmbA/TldD superfamily / Metalloprotease TldD/E, N-terminal domain / Metalloprotease TldD/PmbA, N-terminal / Metalloprotease TldD/PmbA superfamily / Metalloprotease TldD/E, C-terminal domain / Metalloprotease TldD/E, central domain / : / PmbA/TldA metallopeptidase domain 1 / PmbA/TldA metallopeptidase C-terminal domain / PmbA/TldA metallopeptidase central domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metalloprotease PmbA / Metalloprotease TldD
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.35 Å
AuthorsGhilarov, D. / Serebryakova, M. / Stevenson, C.E.M. / Hearnshaw, S.J. / Volkov, D. / Maxwell, A. / Lawson, D.M. / Severinov, K.
Funding support Russian Federation, Poland, United Kingdom, 7items
OrganizationGrant numberCountry
Dynasty foundationPersonal fellowship Russian Federation
Russian Ministry of ScienceResearch and Scientific-Pedagogical Personnel of Innovative Russia in 2009-2013 grant 8591 Russian Federation
Moscow State UniversityDevelopment Program PNG 5.13 Russian Federation
European UnionMarie Sklodowska-Curie grant agreement No. 665778 Poland
Biotechnology and Biological Sciences Research CouncilBB/J016853/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 (MET) United Kingdom
John Innes Foundation United Kingdom
CitationJournal: Structure / Year: 2017
Title: The Origins of Specificity in the Microcin-Processing Protease TldD/E.
Authors: Ghilarov, D. / Serebryakova, M. / Stevenson, C.E.M. / Hearnshaw, S.J. / Volkov, D.S. / Maxwell, A. / Lawson, D.M. / Severinov, K.
History
DepositionMar 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metalloprotease TldD
B: Metalloprotease PmbA
C: Metalloprotease TldD
D: Metalloprotease PmbA
E: VAL-LEU-GLU-ASP-ARG-ILE
F: VAL-LEU-GLU-ASP-ARG-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,02426
Polymers204,4006
Non-polymers1,62420
Water37,5792086
1
A: Metalloprotease TldD
B: Metalloprotease PmbA
E: VAL-LEU-GLU-ASP-ARG-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,01213
Polymers102,2003
Non-polymers81210
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-50 kcal/mol
Surface area34920 Å2
MethodPISA
2
C: Metalloprotease TldD
D: Metalloprotease PmbA
F: VAL-LEU-GLU-ASP-ARG-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,01213
Polymers102,2003
Non-polymers81210
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-52 kcal/mol
Surface area34660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.290, 175.440, 84.330
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUTHRTHRAA3 - 48017 - 494
21LEULEUTHRTHRCC3 - 48017 - 494
12SERSERGLYGLYBB9 - 4499 - 449
22SERSERGLYGLYDD9 - 4499 - 449

NCS ensembles :
ID
1
2

-
Components

-
Metalloprotease ... , 2 types, 4 molecules ACBD

#1: Protein Metalloprotease TldD


Mass: 53033.516 Da / Num. of mol.: 2 / Mutation: E263A,G401D
Source method: isolated from a genetically manipulated source
Details: The TldD protein was expressed with a fourteen residue nickel affinity tag with sequence MGSSHHHHHHSQDP appended to the N-terminus of the full-length amino acid sequence
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: tldD, yhdO, b3244, JW3213 / Plasmid: pCOLADuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star
References: UniProt: P0AGG8, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein Metalloprotease PmbA / Protein TldE


Mass: 48421.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: pmbA, tldE, b4235, JW4194 / Plasmid: pCOLADuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star
References: UniProt: P0AFK0, Hydrolases; Acting on peptide bonds (peptidases)

-
Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide VAL-LEU-GLU-ASP-ARG-ILE


Mass: 744.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Peptide adventitiously bound in the active site. From electron density a match was found to residues 49-54 of TldD, but this identification was not independently verified.
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star

-
Non-polymers , 5 types, 2106 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2086 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: NULL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.525
11-h,-k,l20.475
ReflectionResolution: 1.35→65.29 Å / Num. obs: 403735 / % possible obs: 97.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 13.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Net I/σ(I): 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.35-1.396.91.6230.4290.661.75594.6
6.04-65.297.40.0230.9920.0090.02499.8

-
Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5NJ5

5nj5


Resolution: 1.35→65.29 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.463 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.012 / ESU R Free: 0.011
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1828 19995 5 %RANDOM
Rwork0.145 ---
obs0.1468 383738 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.05 Å2 / Biso mean: 16.998 Å2 / Biso min: 5.39 Å2
Baniso -1Baniso -2Baniso -3
1--18.18 Å20 Å20.52 Å2
2--13.3 Å20 Å2
3---4.88 Å2
Refinement stepCycle: final / Resolution: 1.35→65.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13906 0 102 2179 16187
Biso mean--21.75 27.56 -
Num. residues----1856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01915207
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214126
X-RAY DIFFRACTIONr_angle_refined_deg1.381.96320718
X-RAY DIFFRACTIONr_angle_other_deg0.929332817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99952067
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96924.217645
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.298152576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.52415113
X-RAY DIFFRACTIONr_chiral_restr0.0830.22317
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217752
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023057
X-RAY DIFFRACTIONr_rigid_bond_restr2.49329333
X-RAY DIFFRACTIONr_sphericity_free18.86251571
X-RAY DIFFRACTIONr_sphericity_bonded8.629529633
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A30552
12C30552
21B28202
22D28202
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 1391 -
Rwork0.231 27554 -
all-28945 -
obs--94.61 %

+
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