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- PDB-6nkq: The structure of bovine beta-lactoglobulin in novel crystals grow... -

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Basic information

Entry
Database: PDB / ID: 6nkq
TitleThe structure of bovine beta-lactoglobulin in novel crystals grown at pH 3.8
ComponentsBeta-lactoglobulin
KeywordsUNKNOWN FUNCTION / milk / twinning / space group / whey protein / molecular replacement / Tanford transition
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular space / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMcPherson, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: The structure of bovine beta-lactoglobulin in crystals grown at pH 3.8 exhibiting novel threefold twinning.
Authors: Yeates, T.O. / McPherson, A.
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Beta-lactoglobulin
C: Beta-lactoglobulin
D: Beta-lactoglobulin
E: Beta-lactoglobulin
F: Beta-lactoglobulin
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4657
Polymers119,4256
Non-polymers401
Water1,20767
1
B: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9442
Polymers19,9041
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)19,9041
Polymers19,9041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: Beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)19,9041
Polymers19,9041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: Beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)19,9041
Polymers19,9041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
F: Beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)19,9041
Polymers19,9041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
A: Beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)19,9041
Polymers19,9041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.888, 114.121, 140.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-201-

CA

21B-309-

HOH

31A-202-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
12B
22D
13B
23E
14B
24F
15B
25A
16C
26D
17C
27E
18C
28F
19C
29A
110D
210E
111D
211F
112D
212A
113E
213F
114E
214A
115F
215A

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEGLNGLNBA2 - 15918 - 175
21ILEILEGLNGLNCB2 - 15918 - 175
12VALVALCYSCYSBA3 - 16019 - 176
22VALVALCYSCYSDC3 - 16019 - 176
13ILEILEGLNGLNBA2 - 15918 - 175
23ILEILEGLNGLNED2 - 15918 - 175
14VALVALCYSCYSBA3 - 16019 - 176
24VALVALCYSCYSFE3 - 16019 - 176
15THRTHRCYSCYSBA4 - 16020 - 176
25THRTHRCYSCYSAF4 - 16020 - 176
16VALVALGLNGLNCB3 - 15919 - 175
26VALVALGLNGLNDC3 - 15919 - 175
17ILEILECYSCYSCB2 - 16018 - 176
27ILEILECYSCYSED2 - 16018 - 176
18VALVALGLNGLNCB3 - 15919 - 175
28VALVALGLNGLNFE3 - 15919 - 175
19THRTHRGLNGLNCB4 - 15920 - 175
29THRTHRGLNGLNAF4 - 15920 - 175
110VALVALGLNGLNDC3 - 15919 - 175
210VALVALGLNGLNED3 - 15919 - 175
111VALVALHISHISDC3 - 16119 - 177
211VALVALHISHISFE3 - 16119 - 177
112THRTHRCYSCYSDC4 - 16020 - 176
212THRTHRCYSCYSAF4 - 16020 - 176
113VALVALGLNGLNED3 - 15919 - 175
213VALVALGLNGLNFE3 - 15919 - 175
114THRTHRGLNGLNED4 - 15920 - 175
214THRTHRGLNGLNAF4 - 15920 - 175
115THRTHRCYSCYSFE4 - 16020 - 176
215THRTHRCYSCYSAF4 - 16020 - 176

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Beta-lactoglobulin / Beta-LG


Mass: 19904.227 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Plasmid details: Sigma Biochemicals / Tissue: milk / References: UniProt: P02754
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.31 % / Description: thick hexagonal prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: Reservoir of 3 M NaCl buffered with sodium citrate at pH 3.8 - heavy white precipitate formed upon mixing of 30 mg/ml protein in water with reservoir solution. Precipitate was removed by ...Details: Reservoir of 3 M NaCl buffered with sodium citrate at pH 3.8 - heavy white precipitate formed upon mixing of 30 mg/ml protein in water with reservoir solution. Precipitate was removed by centrifugation. The clear remaining 12ul droplet was equilibrated against the reservoir for 12 to 60 hours
PH range: 3.8 - 4.2 / Temp details: range 4 to 37 degrees C

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Data collection

DiffractionMean temperature: 173 K / Ambient temp details: flash frozen in cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.162
11-h,-k,l20.159
11-1/2H-1/2K, 3/2H-1/2K, L30.164
111/2H-1/2K, 3/2H+1/2K, L40.175
111/2H+1/2K, -3/2H+1/2K, L50.158
11-1/2H+1/2K, -3/2H-1/2K, L60.183
ReflectionResolution: 2.2→60 Å / Num. obs: 49538 / % possible obs: 94 % / Redundancy: 45.2 % / Biso Wilson estimate: 93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.031 / Rrim(I) all: 0.209 / Rsym value: 0.19 / Net I/av σ(I): 10.7 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.7 Å / Redundancy: 46.7 % / Rmerge(I) obs: 1.62 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2094 / CC1/2: 0.976 / Rpim(I) all: 0.24 / Rrim(I) all: 1.66 / Rsym value: 1.62 / % possible all: 45.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BEB

1beb


Resolution: 2.3→57.06 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.264 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26097 2327 5.1 %RANDOM
Rwork0.20681 ---
obs0.20974 43606 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 92.982 Å2
Baniso -1Baniso -2Baniso -3
1-110.93 Å20 Å2-1.74 Å2
2--18.76 Å20 Å2
3----129.69 Å2
Refinement stepCycle: 1 / Resolution: 2.3→57.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7519 0 1 67 7587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0137691
X-RAY DIFFRACTIONr_bond_other_d00.0177346
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.64310426
X-RAY DIFFRACTIONr_angle_other_deg1.0221.57717215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7795958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.38325.914350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.061151475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9191518
X-RAY DIFFRACTIONr_chiral_restr0.0280.21031
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021308
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.17213.2463820
X-RAY DIFFRACTIONr_mcbond_other8.17313.2473819
X-RAY DIFFRACTIONr_mcangle_it11.17114.9224767
X-RAY DIFFRACTIONr_mcangle_other11.1714.9214768
X-RAY DIFFRACTIONr_scbond_it6.79213.4283865
X-RAY DIFFRACTIONr_scbond_other6.79113.4273866
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.35715.0375655
X-RAY DIFFRACTIONr_long_range_B_refined15.927258415
X-RAY DIFFRACTIONr_long_range_B_other15.926258416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B47500.12
12C47500.12
21B48100.12
22D48100.12
31B47250.12
32E47250.12
41B47160.13
42F47160.13
51B47960.12
52A47960.12
61C47650.12
62D47650.12
71C48250.11
72E48250.11
81C47440.12
82F47440.12
91C47760.11
92A47760.11
101D47410.12
102E47410.12
111D48040.13
112F48040.13
121D48430.1
122A48430.1
131E47200.12
132F47200.12
141E47310.11
142A47310.11
151F47970.11
152A47970.11
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.559 161 -
Rwork0.343 3096 -
obs--94.21 %

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