[English] 日本語
Yorodumi
- PDB-5ced: Penicillin G Acylated Bd3459 Predatory Endopeptidase from Bdellov... -

+
Open data


ID or keywords:

Loading...

-
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


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) / Ankyrin repeat profile. / Ankyrin repeat region circular 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) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / 3-Layer(bba) Sandwich / Ankyrin repeat-containing domain superfamily / Beta-lactamase/transpeptidase-like / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Benzylpenicillin


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


Mass: 18.015 Da / Num. of mol.: 178 / 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: 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

-
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

-
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

+
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