[English] 日本語
Yorodumi
- PDB-4q6z: LpoB C-terminal domain from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q6z
TitleLpoB C-terminal domain from Escherichia coli
ComponentsPenicillin-binding protein activator LpoB
KeywordsPROTEIN BINDING / mixed alpha-beta / Lipoprotein / Activator of PBP1b / PBP1b / lipidation / outer-membrane
Function / homology
Function and homology information


periplasmic side of cell outer membrane / peptidoglycan biosynthetic process / enzyme regulator activity / regulation of cell shape
Similarity search - Function
Penicillin-binding protein activator LpoB / Peptidoglycan-synthase activator LpoB / ABC-type transport auxiliary lipoprotein component / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Penicillin-binding protein activator LpoB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKing, D.T. / Strynadka, N.C.J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Insights into the Lipoprotein Outer Membrane Regulator of Penicillin-binding Protein 1B.
Authors: King, D.T. / Lameignere, E. / Strynadka, N.C.
History
DepositionApr 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jul 23, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Penicillin-binding protein activator LpoB
B: Penicillin-binding protein activator LpoB


Theoretical massNumber of molelcules
Total (without water)28,4702
Polymers28,4702
Non-polymers00
Water43224
1
A: Penicillin-binding protein activator LpoB


Theoretical massNumber of molelcules
Total (without water)14,2351
Polymers14,2351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Penicillin-binding protein activator LpoB


Theoretical massNumber of molelcules
Total (without water)14,2351
Polymers14,2351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-2 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.930, 96.930, 96.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 78 - 212 / Label seq-ID: 1 - 135

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Penicillin-binding protein activator LpoB / PBP activator LpoB


Mass: 14235.036 Da / Num. of mol.: 2 / Fragment: LpoB C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / UPEC / Gene: lpoB, UTI89_C1233 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1RD49
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris, 2M ammonium sulfate , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 1, 2012
RadiationMonochromator: KOHZU double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→68.54 Å / Num. all: 7758 / Num. obs: 7727 / % possible obs: 99.6 %
Reflection shellResolution: 2.8→2.95 Å / % possible all: 99.3

-
Processing

Software
NameVersionClassification
MxDCdata collection
PHASERMRphasing
REFMAC5.8.0069refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→68.54 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.906 / SU B: 21.966 / SU ML: 0.409 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28859 355 4.6 %RANDOM
Rwork0.22531 ---
obs0.22828 7350 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.961 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→68.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 24 1994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191992
X-RAY DIFFRACTIONr_bond_other_d0.0060.021938
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9512698
X-RAY DIFFRACTIONr_angle_other_deg1.06534432
X-RAY DIFFRACTIONr_chiral_restr0.0640.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022344
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02444
X-RAY DIFFRACTIONr_mcbond_it3.6856.0841078
X-RAY DIFFRACTIONr_mcbond_other3.6866.0821077
X-RAY DIFFRACTIONr_mcangle_it5.9679.1181344
X-RAY DIFFRACTIONr_mcangle_other5.9659.121345
X-RAY DIFFRACTIONr_scbond_it3.9586.488914
X-RAY DIFFRACTIONr_scbond_other3.9566.49915
X-RAY DIFFRACTIONr_scangle_other6.5989.5591355
X-RAY DIFFRACTIONr_long_range_B_refined10.16561.391588
X-RAY DIFFRACTIONr_long_range_B_other10.16361.41589
Refine LS restraints NCS

Ens-ID: 1 / Number: 6604 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.22 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 25 -
Rwork0.314 537 -
obs--100 %

+
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