[English] 日本語
Yorodumi
- PDB-4dy3: crystal structure of Escherichia coli PliG, a periplasmic lysozym... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dy3
Titlecrystal structure of Escherichia coli PliG, a periplasmic lysozyme inhibitor of g-type lysozyme
ComponentsInhibitor of g-type lysozyme
KeywordsHORMONE INHIBITOR / lysozyme inhibitor / g-type lysozyme binding
Function / homology
Function and homology information


lysozyme inhibitor activity / defense response / outer membrane-bounded periplasmic space
Similarity search - Function
Jelly Rolls - #380 / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Inhibitor of g-type lysozyme
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLeysen, S. / Vanheuverzwijn, S. / Van Asten, K. / Vanderkelen, L. / Michiels, C.W. / Strelkov, S.V.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Structural characterization of the PliG lysozyme inhibitor family.
Authors: Leysen, S. / Vanderkelen, L. / Van Asten, K. / Vanheuverzwijn, S. / Theuwis, V. / Michiels, C.W. / Strelkov, S.V.
History
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inhibitor of g-type lysozyme
B: Inhibitor of g-type lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2624
Polymers25,0782
Non-polymers1842
Water6,377354
1
A: Inhibitor of g-type lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6312
Polymers12,5391
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inhibitor of g-type lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6312
Polymers12,5391
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.543, 83.543, 31.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Inhibitor of g-type lysozyme


Mass: 12538.815 Da / Num. of mol.: 2 / Fragment: UNP residues 23-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pliG, ycgK, b1178, JW1167 / Plasmid: pETHSUL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76002
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M sodium acetate pH5.0, 0.15M NaCl, 25% w/v PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 8, 2010
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→19.69 Å / Num. all: 24224 / Num. obs: 22521 / % possible obs: 93 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2712 / Rsym value: 0.437 / % possible all: 91.1

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.69 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 19.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 995 5.1 %RANDOM
Rwork0.1656 ---
obs0.1679 19529 95.77 %-
all-19529 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.867 Å2 / ksol: 0.413 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2952 Å20 Å2-0 Å2
2--1.2952 Å2-0 Å2
3----2.5904 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 12 354 2138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061894
X-RAY DIFFRACTIONf_angle_d0.962558
X-RAY DIFFRACTIONf_dihedral_angle_d13.973728
X-RAY DIFFRACTIONf_chiral_restr0.068260
X-RAY DIFFRACTIONf_plane_restr0.004338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.89480.25041520.21232479X-RAY DIFFRACTION91
1.8948-2.01340.23061370.17422515X-RAY DIFFRACTION92
2.0134-2.16870.22411500.15522589X-RAY DIFFRACTION95
2.1687-2.38660.24731300.1632644X-RAY DIFFRACTION96
2.3866-2.73120.22961320.16952715X-RAY DIFFRACTION98
2.7312-3.4380.19231600.15532727X-RAY DIFFRACTION98
3.438-19.69260.18741340.16312849X-RAY DIFFRACTION99
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)
11.19880.00770.03731.81-0.04362.1920.0344-0.06130.01420.08770.04360.07650.0547-0.1085-0.04160.08120.0257-0.00350.070.02210.081320.7503-34.4152-2.1643
20.84880.34450.27261.68620.38341.7650.0408-0.0527-0.05680.10360.0576-0.1401-0.08070.1061-0.06540.08010.0058-0.00680.0645-0.02120.100821.1647-6.6279-0.2525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

+
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