[English] 日本語
Yorodumi
- PDB-6dcj: LpoA N-terminal domain from Haemophilus influenzae; monoclinic fo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dcj
TitleLpoA N-terminal domain from Haemophilus influenzae; monoclinic form at 1.35 A resolution
ComponentsPenicillin-binding protein activator LpoA
KeywordsBIOSYNTHETIC PROTEIN / peptidoglycan synthesis / TPR-like / outer membrane lipoprotein / PROTEIN BINDING
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
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #650 / Penicillin-binding protein activator LpoA / LppC putative lipoprotein / Periplasmic binding protein-like I / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Penicillin-binding protein activator LpoA
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsVijayalakshmi, J. / Saper, M.A.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structures of the amino-terminal domain of LpoA from Escherichia coli and Haemophilus influenzae.
Authors: Kelley, A. / Vijayalakshmi, J. / Saper, M.A.
#1: Journal: J. Biol. Chem. / Year: 2017
Title: Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution
Authors: Sathiyamoorthy, K. / Vijayalakshmi, J. / Tirupati, B. / Fan, L. / Saper, M.A.
History
DepositionMay 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI
Revision 1.2May 15, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 11, 2023Group: 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: Penicillin-binding protein activator LpoA
B: Penicillin-binding protein activator LpoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5884
Polymers52,5172
Non-polymers712
Water12,304683
1
A: Penicillin-binding protein activator LpoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2942
Polymers26,2581
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein activator LpoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2942
Polymers26,2581
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.988, 36.927, 95.359
Angle α, β, γ (deg.)90.000, 108.084, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

-
Components

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


Mass: 26258.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: lpoA, HI_1655 / Plasmid: pETBlue2
Details (production host): T7 promoter and C-terminal His6 tag
Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) pLacI / References: UniProt: P45299
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Protein was 10 mg/ml in 0.1% beta-mercaptoethanol, 1 mM EDTA, 0.1 mM benzamidine, 20 mM Tris-HCl pH 8.0. Precipitant contained 20% polyethylene glycol 10,000, 0.1 M HEPES pH 7.5. 2 ul ...Details: Protein was 10 mg/ml in 0.1% beta-mercaptoethanol, 1 mM EDTA, 0.1 mM benzamidine, 20 mM Tris-HCl pH 8.0. Precipitant contained 20% polyethylene glycol 10,000, 0.1 M HEPES pH 7.5. 2 ul protein mixed with 2 ul precipitant on silated cover slip and equilibrated over a reservoir containing 1 ml precipitant.
PH range: 7.5-8.0

-
Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Nov 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.35→34.5 Å / Num. obs: 91763 / % possible obs: 90.3 % / Redundancy: 3.28 % / Biso Wilson estimate: 15.58 Å2 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.047 / Χ2: 0.97 / Net I/σ(I): 13.1 / Num. measured all: 303668 / Scaling rejects: 2279
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2% possible all
1.35-1.42.130.2622.960121.0759.9
1.4-1.452.40.2293.775261.174.6
1.45-1.522.850.1844.691350.9990.8
1.52-1.63.520.1515.8101200.9699.4
1.6-1.73.580.1137.5100310.9199.6
1.7-1.833.620.0859.9101330.8999.9
1.83-2.023.660.06213.2100660.8899.6
2.02-2.313.580.04319.6101340.999.3
2.31-2.913.590.03824.7101651.0299.5
2.91-34.53.160.03429.884411.1880.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å34.44 Å
Translation2 Å34.44 Å

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
d*TREK8.0Idata reduction
d*TREK8.0Idata scaling
PHASER2.7.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P29

4p29


Resolution: 1.35→34.44 Å / SU ML: 0.1352 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.9643
RfactorNum. reflection% reflection
Rfree0.1899 7328 8.02 %
Rwork0.1554 --
obs0.1582 91406 90.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.85 Å2
Refinement stepCycle: LAST / Resolution: 1.35→34.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 2 683 4204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643712
X-RAY DIFFRACTIONf_angle_d0.8675046
X-RAY DIFFRACTIONf_chiral_restr0.06570
X-RAY DIFFRACTIONf_plane_restr0.0048678
X-RAY DIFFRACTIONf_dihedral_angle_d13.3151423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.29641520.26051722X-RAY DIFFRACTION56.07
1.37-1.380.28921710.23991830X-RAY DIFFRACTION60.29
1.38-1.40.28371670.22432023X-RAY DIFFRACTION65.81
1.4-1.420.2411970.21832177X-RAY DIFFRACTION70.3
1.42-1.430.26931970.212285X-RAY DIFFRACTION74.92
1.43-1.450.25712150.18582458X-RAY DIFFRACTION80.83
1.45-1.480.23032380.17152679X-RAY DIFFRACTION85.9
1.48-1.50.22722320.15882786X-RAY DIFFRACTION91.43
1.5-1.520.22312700.14933006X-RAY DIFFRACTION97.41
1.52-1.550.18992540.14753062X-RAY DIFFRACTION99.31
1.55-1.570.18482570.14333072X-RAY DIFFRACTION99.28
1.57-1.60.20282940.13773066X-RAY DIFFRACTION99.67
1.6-1.630.17762580.13893036X-RAY DIFFRACTION99.46
1.63-1.660.17192550.14213074X-RAY DIFFRACTION99.55
1.66-1.70.17212860.14063092X-RAY DIFFRACTION99.85
1.7-1.740.18362590.13973084X-RAY DIFFRACTION99.88
1.74-1.780.18882600.13293058X-RAY DIFFRACTION99.85
1.78-1.830.16852650.13883118X-RAY DIFFRACTION99.73
1.83-1.890.18252710.14343027X-RAY DIFFRACTION99.52
1.89-1.950.16572680.14453131X-RAY DIFFRACTION99.44
1.95-2.020.17462800.14023038X-RAY DIFFRACTION99.7
2.02-2.10.17312650.13773078X-RAY DIFFRACTION99.52
2.1-2.190.16142770.12983084X-RAY DIFFRACTION99.35
2.19-2.310.1712540.13173117X-RAY DIFFRACTION99.15
2.31-2.450.16612760.13663075X-RAY DIFFRACTION99.44
2.45-2.640.17892650.14163111X-RAY DIFFRACTION99.56
2.64-2.910.1792710.14563084X-RAY DIFFRACTION99.26
2.91-3.330.16482620.15693069X-RAY DIFFRACTION97.45
3.33-4.190.2082250.17942545X-RAY DIFFRACTION80.71
4.19-34.450.29121870.25872091X-RAY DIFFRACTION64.04

+
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