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- PDB-5nj9: E. coli Microcin-processing metalloprotease TldD/E with DRVY angi... -

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Basic information

Entry
Database: PDB / ID: 5nj9
TitleE. coli Microcin-processing metalloprotease TldD/E with DRVY angiotensin fragment bound
Components
  • (Metalloprotease ...) x 2
  • ASP-ARG-VAL-TYR
KeywordsHYDROLASE / metalloprotease / microcin / CcdA / DNA gyrase
Function / homology
Function and homology information


peptidase complex / regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / : / regulation of extracellular matrix assembly / regulation of renal output by angiotensin ...peptidase complex / regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / : / regulation of extracellular matrix assembly / regulation of renal output by angiotensin / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / renin-angiotensin regulation of aldosterone production / renal system process / positive regulation of macrophage derived foam cell differentiation / positive regulation of extracellular matrix assembly / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of CoA-transferase activity / vasoconstriction / low-density lipoprotein particle remodeling / type 1 angiotensin receptor binding / response to angiotensin / positive regulation of extrinsic apoptotic signaling pathway / Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / positive regulation of protein tyrosine kinase activity / positive regulation of gap junction assembly / blood vessel remodeling / regulation of cardiac conduction / regulation of vasoconstriction / Metabolism of Angiotensinogen to Angiotensins / positive regulation of epithelial to mesenchymal transition / nitric oxide-cGMP-mediated signaling / negative regulation of MAP kinase activity / positive regulation of protein metabolic process / positive regulation of endothelial cell migration / Peptide ligand-binding receptors / kidney development / positive regulation of cytokine production / angiotensin-activated signaling pathway / regulation of cell growth / growth factor activity / serine-type endopeptidase inhibitor activity / PPARA activates gene expression / hormone activity / protein processing / positive regulation of miRNA transcription / regulation of blood pressure / positive regulation of inflammatory response / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / G alpha (q) signalling events / collagen-containing extracellular matrix / regulation of apoptotic process / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / iron ion binding / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / zinc ion binding / extracellular region / cytosol / cytoplasm
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 / Angiotensinogen, serpin domain / Angiotensinogen / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Angiotensinogen / Metalloprotease PmbA / Metalloprotease TldD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.25 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)205,75626
Polymers204,1316
Non-polymers1,62420
Water37,1112060
1
A: Metalloprotease TldD
B: Metalloprotease PmbA
E: ASP-ARG-VAL-TYR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,87813
Polymers102,0663
Non-polymers81210
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-47 kcal/mol
Surface area33860 Å2
MethodPISA
2
C: Metalloprotease TldD
D: Metalloprotease PmbA
F: ASP-ARG-VAL-TYR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,87813
Polymers102,0663
Non-polymers81210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-51 kcal/mol
Surface area33630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.630, 173.530, 82.860
Angle α, β, γ (deg.)90.000, 90.030, 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: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA2 - 48116 - 495
21ALAALACC2 - 48116 - 495
12GLYGLYBB9 - 4499 - 449
22GLYGLYDD9 - 4499 - 449

NCS ensembles :
ID
1
2

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Components

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Metalloprotease ... , 2 types, 4 molecules ACBD

#1: Protein Metalloprotease TldD


Mass: 53091.551 Da / Num. of mol.: 2 / Mutation: 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 K-12 / Gene: tldD, yhdO, b3244, JW3213 / Production host: Escherichia coli BL21(DE3) (bacteria)
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 K-12 / Gene: pmbA, tldE, b4235, JW4194 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AFK0, Hydrolases; Acting on peptide bonds (peptidases)

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide ASP-ARG-VAL-TYR


Mass: 552.601 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: C-terminal fragment of human angiotensin II / Source: (synth.) Homo sapiens (human) / References: UniProt: P01019*PLUS

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Non-polymers , 5 types, 2080 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.: 2060 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.61
11-h,-k,l20.39
ReflectionResolution: 1.25→74.77 Å / Num. obs: 500650 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.056 / Rrim(I) all: 0.145 / Net I/σ(I): 8.5 / Num. measured all: 3363286 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1 / % possible all: 99.7

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all
1.25-1.286.21.8840.2960.8142.057
5.59-74.776.80.0520.9980.0210.056

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5NJ5

5nj5


Resolution: 1.25→74.77 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.84 / SU ML: 0.018 / SU R Cruickshank DPI: 0.0093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.009 / ESU R Free: 0.009
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1822 25030 5 %RANDOM
Rwork0.1494 ---
obs0.151 475619 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 152.37 Å2 / Biso mean: 12.982 Å2 / Biso min: 2.48 Å2
Baniso -1Baniso -2Baniso -3
1--2.38 Å20 Å20.5 Å2
2--0.47 Å20 Å2
3---1.91 Å2
Refinement stepCycle: final / Resolution: 1.25→74.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13907 0 102 2192 16201
Biso mean--17.45 23.89 -
Num. residues----1853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01915254
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214142
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.96320788
X-RAY DIFFRACTIONr_angle_other_deg0.951332872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30852075
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80624.262650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.771152586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.27415112
X-RAY DIFFRACTIONr_chiral_restr0.0940.22318
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023069
X-RAY DIFFRACTIONr_rigid_bond_restr1.275329396
X-RAY DIFFRACTIONr_sphericity_free18.33551448
X-RAY DIFFRACTIONr_sphericity_bonded6.58529825
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
11A32456
12C32456
21B29652
22D29652
LS refinement shellResolution: 1.249→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 1812 -
Rwork0.239 34363 -
all-36175 -
obs--97.51 %

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