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- PDB-5njc: E. coli Microcin-processing metalloprotease TldD/E (TldD E263A mu... -

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Basic information

Entry
Database: PDB / ID: 5njc
TitleE. coli Microcin-processing metalloprotease TldD/E (TldD E263A mutant) with hexapeptide bound
Components
  • (Metalloprotease ...Metalloproteinase) 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 / cytosol / cytoplasm
Similarity search - Function
TldD / Metalloprotease TldD/E, C-terminal domain / Metalloprotease TldD/E, central domain / : / PmbA/TldD fold / PmbA/TldD superfamily / PmbA/TldA metallopeptidase C-terminal domain / Metalloprotease TldD/E, N-terminal domain / Metalloprotease TldD/PmbA, N-terminal / Metalloprotease TldD/PmbA superfamily ...TldD / Metalloprotease TldD/E, C-terminal domain / Metalloprotease TldD/E, central domain / : / PmbA/TldD fold / PmbA/TldD superfamily / PmbA/TldA metallopeptidase C-terminal domain / Metalloprotease TldD/E, N-terminal domain / Metalloprotease TldD/PmbA, N-terminal / Metalloprotease TldD/PmbA superfamily / PmbA/TldA metallopeptidase domain 1 / 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

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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: 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: 0 / Refine code: 0

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

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Components

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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)

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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

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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 / MES (buffer)


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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 2086 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
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: 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

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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 %

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