[English] 日本語
Yorodumi
- PDB-1uz2: The Cys121Ser Mutant of Beta-Lactoglobulin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uz2
TitleThe Cys121Ser Mutant of Beta-Lactoglobulin
ComponentsBETA-LACTOGLOBULIN
KeywordsTRANSPORT PROTEIN / LIPOCALIN / BETA-BARREL / MILK / WHEY RETINOL-BINDING / ALLERGEN
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMcNae, I. / Jayat, D. / Haertle, T. / Holt, C. / Sawyer, L.
Citation
Journal: Biochemistry / Year: 2004
Title: A recombinant C121S mutant of bovine beta-lactoglobulin is more susceptible to peptic digestion and to denaturation by reducing agents and heating.
Authors: Jayat, D. / Gaudin, J.C. / Chobert, J.M. / Burova, T.V. / Holt, C. / McNae, I. / Sawyer, L. / Haertle, T.
#1: Journal: Eur.J.Biochem. / Year: 2001
Title: Crystal Structures of the Bovine Beta-Lactoglobulin in the Orthorhombic Space Group C2221: Structural Differences between Genetic Variants a and B and the Nature of Tanford Transition
Authors: Oliveira, K.M.G. / Valente-Mesquita, V.L. / Botelho, M.M. / Sawyer, L. / Ferreira, S.T. / Polikarpov, I.
#2: Journal: Int.J.Food Sci.Technol. / Year: 1999
Title: Expression of Recombinant Wild Type and Mutant Beta-Lactoglobulin in the Yeast Pichia Pastoris
Authors: Wilson, C. / Quarrie, L. / Allan, G.J. / Flint, D.J. / Sawyer, L. / Holt, C.
History
DepositionMar 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 13, 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
X: BETA-LACTOGLOBULIN


Theoretical massNumber of molelcules
Total (without water)18,3711
Polymers18,3711
Non-polymers00
Water1,26170
1
X: BETA-LACTOGLOBULIN

X: BETA-LACTOGLOBULIN


Theoretical massNumber of molelcules
Total (without water)36,7422
Polymers36,7422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)55.690, 80.470, 66.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

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


Mass: 18371.199 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle)
Description: BETA-LACTOGLOBULIN IS NORMALLY OBTAINED FROM MILK. MATURE CODING SEQUENCE
Variant: A VARIANT / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P02754
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE A VARIANT DIFFERS FROM THE EQUALLY COMMON B-VARIANT AT G64D AND A118V

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.093 Å3/Da / Density % sol: 39.42 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROPS WITH 20 MG/ML PROTEIN PLUS APPROX 2M AMMONIUM SULPHATE, 10MM HEPES, PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2003 / Details: MIRRORS
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.95→46 Å / Num. obs: 11241 / % possible obs: 99.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 5.7
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QG5

1qg5


Resolution: 1.95→45.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.567 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS ADDED IN THEIR RIDING POSITIONS. AS USUAL WITH COW LACTOGLOBULIN STRUCTURES THERE ARE SEVERAL INDISTINCT SURFACE LOOPS PRINCIPALLY AROUND 64, 88, 114 AND AFTER 152. THE DISULPHIDE ...Details: HYDROGENS ADDED IN THEIR RIDING POSITIONS. AS USUAL WITH COW LACTOGLOBULIN STRUCTURES THERE ARE SEVERAL INDISTINCT SURFACE LOOPS PRINCIPALLY AROUND 64, 88, 114 AND AFTER 152. THE DISULPHIDE BRIDGE BETWEEN C66 AND C160 HAS VIRTUALLY NO ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 577 5.2 %RANDOM
Rwork0.267 ---
obs0.213 10574 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.58 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å20 Å2
2--4.31 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 0 70 1322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221276
X-RAY DIFFRACTIONr_bond_other_d0.0020.021189
X-RAY DIFFRACTIONr_angle_refined_deg2.0611.9951728
X-RAY DIFFRACTIONr_angle_other_deg1.00832800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1675157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.140.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021368
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02209
X-RAY DIFFRACTIONr_nbd_refined0.2250.2235
X-RAY DIFFRACTIONr_nbd_other0.2470.21292
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0940.2790
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2040.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.421.5794
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.52721290
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3283482
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7774438
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.204 42
Rwork0.231 783

+
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