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- PDB-5ced: Penicillin G Acylated Bd3459 Predatory Endopeptidase from Bdellov... -

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Basic information

Entry
Database: PDB / ID: 5ced
TitlePenicillin G Acylated Bd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity protein Bd3460
Components
  • Bd3459
  • Bd3460
KeywordsHYDROLASE / transpeptidase and ankyrin repeat / hydrolae / protein binding
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 / Ankyrin repeats (3 copies) / 3-Layer(bba) Sandwich / 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 / Ankyrin repeats (3 copies) / 3-Layer(bba) Sandwich / 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
OPEN FORM - PENICILLIN G / Uncharacterized protein / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bd3459
B: Bd3460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3113
Polymers73,9752
Non-polymers3361
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint0 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.540, 59.160, 192.040
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 HD100 (bacteria)
Gene: Bd3459 / Production host: Escherichia coli BL21(DE3) (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 HD100 (bacteria)
Gene: Bd3460 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MHS9
#3: Chemical ChemComp-PNM / OPEN FORM - PENICILLIN G


Mass: 336.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 37.85 %
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: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.02→100 Å / Num. obs: 37468 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rsym value: 0.067 / Net I/σ(I): 16.2
Reflection shellRsym value: 0.672

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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: 5cec

5cec


Resolution: 2.02→96.02 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.891 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 1977 5 %RANDOM
Rwork0.1716 ---
obs0.1733 37468 99.85 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.07 Å2 / Biso mean: 45.436 Å2 / Biso min: 12.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å2-0 Å2
2--2.09 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 2.02→96.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 249 178 4827
Biso mean--45.44 39.67 -
Num. residues----543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024491
X-RAY DIFFRACTIONr_bond_other_d0.0020.024408
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9726047
X-RAY DIFFRACTIONr_angle_other_deg1.003310167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0735572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63525.967181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59915840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1891513
X-RAY DIFFRACTIONr_chiral_restr0.1350.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025066
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02955
X-RAY DIFFRACTIONr_mcbond_it1.2722.1622299
X-RAY DIFFRACTIONr_mcbond_other1.272.1622298
X-RAY DIFFRACTIONr_mcangle_it1.9483.2362863
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 151 -
Rwork0.266 2734 -
all-2885 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6489-0.06560.15783.22171.50813.33290.0456-0.12120.0483-0.0052-0.11190.5719-0.302-0.47360.06620.06230.04030.07230.0901-0.01580.2291-31.262-0.134-26.468
22.03910.80321.31263.1202-0.06567.24350.1102-0.1617-0.05410.3524-0.0225-0.46060.28270.2184-0.08770.3239-0.02380.04490.1812-0.12870.2257-8.0512.6544.106
311.6533-7.67290.18685.2593-1.4218.46790.31780.5083-0.2851-0.3371-0.37280.11060.780.55210.0550.84490.0032-0.03580.5872-0.25730.6295-8.405-8.631-0.272
410.0873-6.67375.380817.9564-4.02275.63480.24930.6573-0.2347-1.0535-0.3634-0.34370.24961.21670.11410.3703-0.04820.26370.4654-0.06690.38870.5696.108-11.571
52.14970.49691.1574.3206-1.78277.01670.1627-0.5097-0.25040.5172-0.0699-0.42610.38260.0797-0.09280.4626-0.04940.03010.303-0.10750.2946-8.7121.8727.206
62.5610.053-0.35972.03080.07943.61850.1104-0.3511-0.02710.2541-0.01820.2384-0.1498-0.2402-0.09220.1160.00490.08230.095-0.02990.1663-25.827-0.14-20.627
72.8383-1.0936-0.97134.0848-0.6383.20520.17370.0867-0.0055-0.0759-0.09580.238-0.1398-0.1929-0.07790.01410.0131-0.00490.0245-0.02470.072-23.764-4.292-35.184
81.2544-0.07093.09750.25020.730312.3475-0.0446-0.08790.2213-0.030.0645-0.0462-0.8440.1674-0.01990.3483-0.07970.10150.0785-0.06730.3193-14.13912.539-19.067
97.55855.4549-7.67423.17779.481519.5236-0.65090.1292-0.65940.78290.1536-0.63911.6413-0.13340.49730.40570.0801-0.03180.40150.20030.3776-6.825-28.975-25.089
1011.4529-0.51682.099211.01650.727211.20850.2532-1.2188-1.05750.8874-0.0598-0.41681.00330.3964-0.19350.37650.1052-0.03980.50080.13280.2028-2.856-22.009-19.968
115.49030.44070.95893.08930.36343.3483-0.0351-0.4828-0.35630.2446-0.0461-0.21220.18260.26630.08110.12280.0819-0.02140.12320.02580.1294-2.754-19.709-31.4
123.1908-0.1815-0.05533.3337-0.95925.362-0.0766-0.08090.2520.0443-0.0931-0.2985-0.07240.44860.16970.02860.0199-0.02010.0642-0.00840.0938-4.714-10.435-38.562
134.8636-0.2351-0.22254.3394-0.23066.08080.0893-0.10120.2331-0.1005-0.1295-0.3399-0.330.48160.04020.0625-0.00450.00630.05410.01660.1076-4.453-3.405-44.9
143.77020.1041-0.86473.2240.60462.96940.0320.01560.0709-0.18820.0452-0.1745-0.130.1978-0.07720.0778-0.01930.00290.03660.02940.0634-10.3921.688-51.323
156.1997-0.8505-0.26199.92383.0428.2798-0.09590.70040.1423-0.59580.1996-0.01270.0672-0.1405-0.10370.1499-0.0007-0.03620.12130.03080.0574-15.566-0.321-60.701
168.47120.9002-6.07574.1472-1.51168.74860.45320.10390.64130.1603-0.17010.0038-0.6389-0.0053-0.28320.11710.04130.00240.07730.07280.1879-18.20210.128-54.87
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 88
2X-RAY DIFFRACTION2A89 - 145
3X-RAY DIFFRACTION3A146 - 184
4X-RAY DIFFRACTION4A185 - 204
5X-RAY DIFFRACTION5A205 - 239
6X-RAY DIFFRACTION6A240 - 359
7X-RAY DIFFRACTION7A360 - 410
8X-RAY DIFFRACTION8A411 - 438
9X-RAY DIFFRACTION9B27 - 33
10X-RAY DIFFRACTION10B34 - 53
11X-RAY DIFFRACTION11B54 - 96
12X-RAY DIFFRACTION12B97 - 129
13X-RAY DIFFRACTION13B130 - 156
14X-RAY DIFFRACTION14B157 - 189
15X-RAY DIFFRACTION15B190 - 201
16X-RAY DIFFRACTION16B202 - 220

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