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- PDB-5cec: Bd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus in... -

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Basic information

Entry
Database: PDB / ID: 5cec
TitleBd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity protein Bd3460
Components
  • Bd3459
  • Bd3460
KeywordsPROTEIN BINDING / transpeptidase and ankyrin repeat
Function / homology
Function and homology information


peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / proteolysis
Similarity search - Function
D-Ala-D-Ala carboxypeptidase C, peptidase S13 / Peptidase S13, D-Ala-D-Ala carboxypeptidase C / D-Ala-D-Ala carboxypeptidase 3 (S13) family / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Ankyrin repeat-containing domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(bba) Sandwich / Ankyrin repeats (3 copies) / Ankyrin repeat profile. ...D-Ala-D-Ala carboxypeptidase C, peptidase S13 / Peptidase S13, D-Ala-D-Ala carboxypeptidase C / D-Ala-D-Ala carboxypeptidase 3 (S13) family / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Ankyrin repeat-containing domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(bba) Sandwich / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Beta-lactamase/transpeptidase-like / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsLovering, A.L. / Cadby, I.T. / Lambert, C. / Sockett, R.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J015229/1 United Kingdom
CitationJournal: Nat Commun / Year: 2015
Title: Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus.
Authors: Lambert, C. / Cadby, I.T. / Till, R. / Bui, N.K. / Lerner, T.R. / Hughes, W.S. / Lee, D.J. / Alderwick, L.J. / Vollmer, W. / Sockett, E.R. / Lovering, A.L.
History
DepositionJul 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_audit_support / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bd3459
B: Bd3460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5518
Polymers73,9752
Non-polymers5766
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-76 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.610, 59.170, 192.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bd3459


Mass: 49219.406 Da / Num. of mol.: 1 / Fragment: Bd3459 / Mutation: K38M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria)
Gene: Bd3459 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q6MHT0, serine-type D-Ala-D-Ala carboxypeptidase
#2: Protein Bd3460


Mass: 24755.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria)
Gene: Bd3460 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6MHS9
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 38.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M citrate pH 5.0, 3.2M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.36→100 Å / Num. obs: 117291 / % possible obs: 97.2 % / Redundancy: 6 % / Rsym value: 0.032 / Net I/σ(I): 23.4
Reflection shellRsym value: 0.516

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CEA & 5CEB

5cea

5ceb


Resolution: 1.36→96.14 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.737 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1688 6194 5 %RANDOM
Rwork0.1412 ---
obs0.1426 117290 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.9 Å2 / Biso mean: 23.69 Å2 / Biso min: 12.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å2-0 Å20 Å2
2--1.19 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 1.36→96.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4549 0 30 493 5072
Biso mean--40.83 32.26 -
Num. residues----594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024660
X-RAY DIFFRACTIONr_bond_other_d0.0020.024544
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9726290
X-RAY DIFFRACTIONr_angle_other_deg0.923310498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5795600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55426.085189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26115873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3761513
X-RAY DIFFRACTIONr_chiral_restr0.0910.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025254
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02977
X-RAY DIFFRACTIONr_mcbond_it1.3892.0712382
X-RAY DIFFRACTIONr_mcbond_other1.3892.0722381
X-RAY DIFFRACTIONr_mcangle_it1.873.1192976
X-RAY DIFFRACTIONr_rigid_bond_restr1.74439204
X-RAY DIFFRACTIONr_sphericity_free25.1445162
X-RAY DIFFRACTIONr_sphericity_bonded10.84659471
LS refinement shellResolution: 1.36→1.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 357 -
Rwork0.225 6775 -
all-7132 -
obs--76.7 %

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