[English] 日本語
Yorodumi
- PDB-7za0: Mutant L58F of recombinant bovine beta-lactoglobulin in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7za0
TitleMutant L58F of recombinant bovine beta-lactoglobulin in complex with pramocaine
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lactoglobulin / ligand / mutation / pramocaine
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin signature.
Similarity search - Domain/homology
Pramocaine / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLoch, J.I. / Kurpiewska, K. / Bonarek, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Recognit. / Year: 2023
Title: beta-Lactoglobulin variants as potential carriers of pramoxine: Comprehensive structural and biophysical studies.
Authors: Bonarek, P. / Mularczyk, D. / Loch, J.I. / Kurpiewska, K. / Dziedzicka-Wasylewska, M.
History
DepositionMar 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6563
Polymers18,2671
Non-polymers3892
Water2,342130
1
AAA: Beta-lactoglobulin
hetero molecules

AAA: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3136
Polymers36,5342
Non-polymers7794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)53.722, 53.722, 112.254
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18267.031 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L58F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: LGB / Plasmid: pET-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P02754
#2: Chemical ChemComp-PX9 / Pramocaine


Mass: 293.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.2 M ammonium sulfate in 0.5 M Tris-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54056 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Feb 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.1→13.84 Å / Num. obs: 11346 / % possible obs: 99 % / Redundancy: 2.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.052 / Net I/σ(I): 9.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 933 / CC1/2: 0.78 / Rrim(I) all: 0.491 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy


Resolution: 2.1→13.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.388 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.204 / ESU R Free: 0.179
RfactorNum. reflection% reflection
Rfree0.2242 1058 9.342 %
Rwork0.1747 10267 -
all0.179 --
obs-11325 98.401 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.695 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å2-0 Å2
3----0.585 Å2
Refinement stepCycle: LAST / Resolution: 2.1→13.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 26 130 1371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131262
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161244
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.6481702
X-RAY DIFFRACTIONr_angle_other_deg1.2391.5832887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7155150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03625.53656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51115238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.611153
X-RAY DIFFRACTIONr_chiral_restr0.0810.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021361
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02245
X-RAY DIFFRACTIONr_nbd_refined0.1940.2202
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.21120
X-RAY DIFFRACTIONr_nbtor_refined0.1590.2571
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.277
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0480.22
X-RAY DIFFRACTIONr_nbd_other0.2290.218
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.210
X-RAY DIFFRACTIONr_mcbond_it2.3072.918609
X-RAY DIFFRACTIONr_mcbond_other2.3072.917608
X-RAY DIFFRACTIONr_mcangle_it3.6164.348756
X-RAY DIFFRACTIONr_mcangle_other3.6144.349757
X-RAY DIFFRACTIONr_scbond_it2.93.434653
X-RAY DIFFRACTIONr_scbond_other2.8983.415650
X-RAY DIFFRACTIONr_scangle_it4.8314.954946
X-RAY DIFFRACTIONr_scangle_other4.8384.919941
X-RAY DIFFRACTIONr_lrange_it6.73634.6471303
X-RAY DIFFRACTIONr_lrange_other6.61334.2981284
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1540.292700.2667490.2688360.8120.80797.96650.269
2.154-2.2110.334900.2526870.267870.8180.86198.72940.251
2.211-2.2740.24510.2216980.2237540.8970.89699.33690.218
2.274-2.3420.26570.2167050.227730.8890.90598.5770.211
2.342-2.4160.261540.2096570.2137160.8860.91699.30170.201
2.416-2.4980.25660.1976350.2027060.9250.9399.29180.184
2.498-2.5890.328650.2026320.2136990.850.91199.71390.187
2.589-2.6910.291610.2055930.2146590.9020.91699.24130.191
2.691-2.8060.257780.1925510.26290.9230.9351000.178
2.806-2.9370.206460.1475700.1526160.960.9641000.134
2.937-3.0880.219420.175390.1735810.9410.9541000.158
3.088-3.2650.259500.174980.1785480.9270.9451000.163
3.265-3.4770.194620.1624790.1665430.9550.96299.63170.155
3.477-3.7360.196720.164220.1654970.960.96799.39640.155
3.736-4.0630.183430.1494160.1524640.9590.96998.92240.145
4.063-4.4940.159460.1323750.1344270.9680.9898.59480.126
4.494-5.10.179310.1263380.133800.9680.98297.10530.123
5.1-6.0450.224210.2113150.2123460.9390.95197.10980.208
6.045-7.8340.37280.1732430.1892860.8970.96294.75520.169
7.834-13.840.164250.1661650.1662070.9690.97591.78740.162
Refinement TLS params.Method: refined / Origin x: -15.5929 Å / Origin y: 4.6352 Å / Origin z: 3.5473 Å
111213212223313233
T0.1676 Å2-0.0416 Å2-0.0183 Å2-0.0488 Å20.0226 Å2--0.0139 Å2
L0.2099 °20.3531 °20.1793 °2-0.9988 °20.3613 °2--1.3613 °2
S-0.1518 Å °0.0428 Å °0.0352 Å °-0.1061 Å °0.0566 Å °0.0819 Å °-0.047 Å °0.1638 Å °0.0952 Å °
Refinement TLS groupSelection: ALL

+
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