[English] 日本語
Yorodumi
- PDB-1gx9: BOVINE BETA-LACTOGLOBULIN COMPLEXED WITH RETINOIC ACID, TRIGONAL ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gx9
TitleBOVINE BETA-LACTOGLOBULIN COMPLEXED WITH RETINOIC ACID, TRIGONAL LATTICE Z
ComponentsBETA-LACTOGLOBULIN
KeywordsLIPOCALIN / MILK / WHEY TRANSPORT / BOVINE / RETINOL-BINDING ALLERGEN / RETINOIC ACID-BINDING
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 beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RETINOIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsKontopidis, G. / Sawyer, L.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The Ligand-Binding Site of Bovine Beta-Lactoglobulin: Evidence for a Function?
Authors: Kontopidis, G. / Holt, C. / Sawyer, L.
History
DepositionMar 29, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2002Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Dec 13, 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
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-LACTOGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6022
Polymers18,3011
Non-polymers3001
Water2,504139
1
A: BETA-LACTOGLOBULIN
hetero molecules

A: BETA-LACTOGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2034
Polymers36,6022
Non-polymers6012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)53.660, 53.660, 111.225
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2117-

HOH

DetailsTHE DIMER GIVEN HERE IS PHYSIOLOGICAL DIMERTHE STRAND AA10 CREATES A CONTINUOUS BETA SHEET BETWEENRESIDUES 147-150 IN THE DIMER

-
Components

#1: Protein BETA-LACTOGLOBULIN / BETA-LG / ALLERGEN BOS D 5


Mass: 18301.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PROTEIN PURCHASED FROM SIGMA CHEMICALS, CAT.NO. L8005
Source: (natural) BOS TAURUS (domestic cattle) / Organ: MAMMARY GLAND / Variant: GENETIC VARIANT B / References: UniProt: P02754
#2: Chemical ChemComp-REA / RETINOIC ACID


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.495 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 290 K / pH: 7.3
Details: 17 DEG C, 8MUL BLG-RET COMPLEX 20MM TRIS, PH 8 + 8MUL NA CITRATE 1.25M, 0.1M HEPES, PH7.3, PER DROP
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMTris1droppH8.0
220 mg/mlprotein1drop
31.25 Msodium citrate1reservoir
40.1 MHEPES1reservoirpH7.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.542
DetectorType: RAYONIX MX340-HS / Detector: CCD / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.34→15 Å / Num. obs: 8213 / % possible obs: 99.6 % / Redundancy: 16.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.3
Reflection shellRmerge(I) obs: 0.25 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 138409
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.25

-
Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B0O

1b0o


Resolution: 2.34→15 Å / Num. parameters: 5758 / Num. restraintsaints: 5312 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: THE RESIDUE, LEU 1 IS NOT OBSERVED
RfactorNum. reflection% reflectionSelection details
Rfree0.298 400 5 %RANDOM
all0.2271 7813 --
obs0.2259 -94.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1439.5
Refinement stepCycle: LAST / Resolution: 2.34→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 22 139 1433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0224
X-RAY DIFFRACTIONs_zero_chiral_vol0.019
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.027
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.122
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.227 / Rfactor obs: 0.298 / Rfactor Rfree: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_bond_d / Dev ideal: 0.005

+
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