4CK4 | pdb_00004ck4

Ovine beta-Lactoglobulin at Atomic Resolution

PDB DOI: https://doi.org/10.2210/pdb4CK4/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Ovis aries
Mutation(s): Yes

Deposited: 2013-12-27 Released: 2014-10-08
Deposition Author(s): Kontopidis, G., Nordle, A., Sawyer, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free:
0.169 (Depositor), 0.196 (DCC)
R-Value Work:
0.139 (Depositor)
R-Value Observed:
0.141 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Ovine Beta-Lactoglobulin at Atomic Resolution

Kontopidis, G., Nordle Gilliver, A., Sawyer, L.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 1498

PubMed: 25372816 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X14020950
Primary Citation Related Structures:
4CK4

PubMed Abstract:
The crystal structure of the triclinic form of the milk protein β-lactoglobulin from sheep (Ovis aries) at 1.1 Å resolution is described together with a comparison of the triclinic structures of the low-pH bovine and high-pH ovine proteins. All three structures are remarkably similar, despite the well known pH-dependent conformational transition described for the bovine and porcine proteins that occurs in solution. The high resolution of the present structure determination has allowed a more accurate description of the protein than has hitherto been possible, but it is still not clear whether flexibility changes in the external loops can compensate for the presence of a significant void in the unliganded interior of the structure.

Organizational Affiliation

Structural Biochemistry Group, Institute of Cell and Molecular Biology, The University of Edinburgh, Swann Building, King's Buildings, Mayfield Road, Edinburgh EH10 3BF, Scotland.

Macromolecule Content

Total Structure Weight: 37.26 kDa
Atom Count: 3,306
Modeled Residue Count: 323
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA_LACTOGLOBULIN-1/B	A, B	162	Ovis aries	Mutation(s): 1
UniProt
Find proteins for P67976 (Ovis aries) Explore P67976 Go to UniProtKB: P67976
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P67976
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain C [auth A] MOL2 format, chain P [auth B] MOL2 format, chain C [auth A] mmCIF format, chain P [auth B] mmCIF format, chain C [auth A]	C [auth A], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain P [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A], M [auth A], Y [auth B], Z [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B], BA [auth B], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain N [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain N [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain CA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain CA [auth B]	CA [auth B], O [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain O [auth A] Interactions & Density Focus chain CA [auth B] Focus chain O [auth A]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free: 0.169 (Depositor), 0.196 (DCC)
R-Value Work: 0.139 (Depositor)
R-Value Observed: 0.141 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.148	α = 69.75
b = 49.031	β = 69.08
c = 49.053	γ = 77.56

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-10-08

Deposition Author(s):

Kontopidis, G.

Nordle, A.

Sawyer, L.

Revision History (Full details and data files)

Version 1.0: 2014-10-08
Type: Initial release
Version 1.1: 2014-11-12
Changes: Database references
Version 1.2: 2015-02-25
Changes: Database references
Version 1.3: 2015-05-27
Changes: Atomic model, Other
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.5: 2024-11-13
Changes: Structure summary