[English] 日本語
Yorodumi
- PDB-2akq: The structure of bovine B-lactoglobulin A in crystals grown at ve... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2akq
TitleThe structure of bovine B-lactoglobulin A in crystals grown at very low ionic strength
ComponentsBeta-lactoglobulin variant A
KeywordsTRANSPORT PROTEIN / B-lactoglbulin / crystal lattice / low ionic strength / pseudo-merohedral twinning
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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAdams, J.J. / Anderson, B.F. / Norris, G.E. / Creamer, L.K. / Jameson, G.B.
Citation
Journal: J.Struct.Biol. / Year: 2006
Title: Structure of bovine beta-lactoglobulin (variant A) at very low ionic strength
Authors: Adams, J.J. / Anderson, B.F. / Norris, G.E. / Creamer, L.K. / Jameson, G.B.
#1: Journal: Structure / Year: 1997
Title: Bovine beta-lactoglobulin at 1.8 A resolution--still an enigmatic lipocalin
Authors: Brownlow, S. / Morais-Cabral, J.H. / Cooper, R. / Flower, D.R. / Yewdall, S.J. / Polikarpov, I. / North, A.C. / Sawyer, L.
#2: Journal: Biochemistry / Year: 1998
Title: Structural basis of the Tanford transition of bovine beta-lactoglobulin
Authors: Qin, B.Y. / Bewley, M.C. / Creamer, L.K. / Baker, H.M. / Baker, E.N. / Jameson, G.B.
#3: Journal: Febs Lett. / Year: 1998
Title: 12-Bromododecanoic acid binds inside the calyx of bovine beta-lactoglobulin
Authors: Qin, B.Y. / Creamer, L.K. / Baker, E.N. / Jameson, G.B.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 16, 2005ID: 1MFH
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 1.4Oct 23, 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
A: Beta-lactoglobulin variant A
B: Beta-lactoglobulin variant A
C: Beta-lactoglobulin variant A
D: Beta-lactoglobulin variant A


Theoretical massNumber of molelcules
Total (without water)73,5494
Polymers73,5494
Non-polymers00
Water1,22568
1
A: Beta-lactoglobulin variant A
B: Beta-lactoglobulin variant A


Theoretical massNumber of molelcules
Total (without water)36,7752
Polymers36,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta-lactoglobulin variant A

C: Beta-lactoglobulin variant A


Theoretical massNumber of molelcules
Total (without water)36,7752
Polymers36,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x+1/2,-y+3/2,-z1
3
D: Beta-lactoglobulin variant A

D: Beta-lactoglobulin variant A


Theoretical massNumber of molelcules
Total (without water)36,7752
Polymers36,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x+1/2,-y+3/2,-z+11
Unit cell
Length a, b, c (Å)68.191, 68.231, 131.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Beta-lactoglobulin variant A / Beta-LG / Allergen Bos d 5


Mass: 18387.264 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: MAMMARY GLAND / References: UniProt: P02754
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIN THE SWISS-PROT ENTRY, THE 64TH RESIDUE IS GLY, THE 118TH IS ALA. IN VARIANT A, THE 64TH IS ASP ...IN THE SWISS-PROT ENTRY, THE 64TH RESIDUE IS GLY, THE 118TH IS ALA. IN VARIANT A, THE 64TH IS ASP AND THE 118TH IS VAL.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 295 K / Method: microdialysis / pH: 5.2
Details: Ultra pure water, pH 5.20, MICRODIALYSIS, temperature 295K

-
Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 15, 2001
RadiationMonochromator: AXCO P50 FOCUSSING CAPILLARY / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 12501 / Num. obs: 12501 / % possible obs: 92.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 12 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3 / Num. unique all: 1162 / % possible all: 94.3

-
Processing

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

1beb


Resolution: 3→10 Å / Num. parameters: 19369 / Num. restraintsaints: 35963 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: This entry is a revision of 1mfh, taking into account 2 the effects of twinning. The twin law is (0 1 0/1 0 0/0 0 -1) R 3 is 0.325. Essentially addition of one parameter for twinning 4 ...Details: This entry is a revision of 1mfh, taking into account 2 the effects of twinning. The twin law is (0 1 0/1 0 0/0 0 -1) R 3 is 0.325. Essentially addition of one parameter for twinning 4 reduced R(working) from 0.293 to 0.224 and R(free) from 0.316 5 to 0.266. About torsion angles outside the expected ramachandran regions, TYR 99 is the central residue of a gamma turn characteristic of beta-lactoglobulins. ALA 34 is part of the dimer interface.
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 605 5 %RANDOM
Rwork0.2241 ---
all0.2262 12501 --
obs0.2143 10510 92.6 %-
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5017.5
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4987 0 0 68 5055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.006
X-RAY DIFFRACTIONs_similar_dist0.017
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.019
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.022
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.07
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.013
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 3→3 Å
RfactorNum. reflection% reflection
Rwork0.272 --
obs-1162 49.6 %

+
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