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- PDB-7bf8: Mutant I56F of recombinant bovine beta-lactoglobulin in complex w... -

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Basic information

Entry
Database: PDB / ID: 7bf8
TitleMutant I56F of recombinant bovine beta-lactoglobulin in complex with tetracaine
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lactoglobulin / mutant / ligand
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 / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin signature.
Similarity search - Domain/homology
Tetracaine / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLoch, J.I. / Kaczor, K. / Lewinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2012/05/B/ST5/00278 Poland
CitationJournal: Acta Biochim.Pol. / Year: 2021
Title: Interactions of new lactoglobulin variants with tetracaine: crystallographic studies of ligand binding to lactoglobulin mutants possessing single substitution in the binding pocket.
Authors: Loch, J. / Bonarek, P. / Siuda, M. / Wrobel, P. / Lewinski, K.
History
DepositionJan 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_radiation_wavelength / diffrn_source
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 / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Beta-lactoglobulin
BBB: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0876
Polymers36,5342
Non-polymers5534
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-39 kcal/mol
Surface area14610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.831, 69.665, 79.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 3 - 162 / Label seq-ID: 3 - 162

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18267.031 Da / Num. of mol.: 2 / Mutation: L1A, I2S, I56F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: LGB / Plasmid: pET-Duet / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Origamim B (DE3) / References: UniProt: P02754
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TE4 / Tetracaine / 2-(dimethylamino)ethyl 4-(butylamino)benzoate


Mass: 264.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.4 M ammonium sulfate in 0.5 M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.5406 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jan 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.8→14.62 Å / Num. obs: 28251 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.051 / Rrim(I) all: 0.12 / Net I/σ(I): 12.3 / Num. measured all: 152301 / Scaling rejects: 1581
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.844.10.8121.5678916500.7010.4550.9331.5100
9-14.624.90.0379862010.9990.0160.0451.376

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy


Resolution: 1.8→14.62 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.951 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.145 / ESU R Free: 0.129
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 1032 3.658 %RANDOM
Rwork0.1915 27180 --
all0.193 ---
obs0.19264 28212 99.745 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.566 Å2
Baniso -1Baniso -2Baniso -3
1--0.006 Å20 Å20 Å2
2--0.014 Å2-0 Å2
3----0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.8→14.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 34 318 2748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132486
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172426
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.6493370
X-RAY DIFFRACTIONr_angle_other_deg1.3731.5935619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7465306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.60325.327107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87815462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.131156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022719
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02487
X-RAY DIFFRACTIONr_nbd_refined0.1910.2404
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22204
X-RAY DIFFRACTIONr_nbtor_refined0.160.21120
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21193
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2230
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.219
X-RAY DIFFRACTIONr_nbd_other0.2640.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.232
X-RAY DIFFRACTIONr_mcbond_it0.961.1431221
X-RAY DIFFRACTIONr_mcbond_other0.9551.1421220
X-RAY DIFFRACTIONr_mcangle_it1.641.6981519
X-RAY DIFFRACTIONr_mcangle_other1.6411.6991520
X-RAY DIFFRACTIONr_scbond_it1.2431.2921265
X-RAY DIFFRACTIONr_scbond_other1.2441.2771254
X-RAY DIFFRACTIONr_scangle_it2.0521.8811848
X-RAY DIFFRACTIONr_scangle_other2.0561.8581831
X-RAY DIFFRACTIONr_lrange_it4.34214.3062662
X-RAY DIFFRACTIONr_lrange_other4.30714.062635
X-RAY DIFFRACTIONr_ncsr_local_group_10.130.054401
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.130340.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.130340.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.271800.2591956X-RAY DIFFRACTION100
1.847-1.8970.243850.2421905X-RAY DIFFRACTION100
1.897-1.9520.248580.2131911X-RAY DIFFRACTION100
1.952-2.0120.241810.2091816X-RAY DIFFRACTION100
2.012-2.0780.243670.1971777X-RAY DIFFRACTION100
2.078-2.1510.214630.1941722X-RAY DIFFRACTION100
2.151-2.2320.212510.1831667X-RAY DIFFRACTION100
2.232-2.3230.2460.1871630X-RAY DIFFRACTION100
2.323-2.4260.228610.1891519X-RAY DIFFRACTION100
2.426-2.5440.319590.2041468X-RAY DIFFRACTION100
2.544-2.6810.195570.1861415X-RAY DIFFRACTION100
2.681-2.8440.26510.2021338X-RAY DIFFRACTION100
2.844-3.0390.29400.1891263X-RAY DIFFRACTION100
3.039-3.2820.194450.171165X-RAY DIFFRACTION100
3.282-3.5940.194430.1651094X-RAY DIFFRACTION100
3.594-4.0150.215400.177988X-RAY DIFFRACTION100
4.015-4.6320.149380.148874X-RAY DIFFRACTION100
4.632-5.6620.207250.167766X-RAY DIFFRACTION100
5.662-7.9610.214230.208608X-RAY DIFFRACTION100
7.961-14.620.205190.201291X-RAY DIFFRACTION81.3648
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.79420.2994-0.10590.7583-0.13020.0769-0.01340.04470.03860.05280.02560.0597-0.00270.0351-0.01220.0202-0.00230.0030.040.00170.005114.97357.09532.1609
20.91560.35060.12340.48040.09760.1668-0.0207-0.0089-0.02630.00380.0028-0.0287-0.0015-0.01860.01790.01770.00140.00580.02370.00010.0083-13.7314-6.914431.465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA2 - 162
2X-RAY DIFFRACTION1ALLAAA301 - 463
3X-RAY DIFFRACTION2ALLBBB3 - 162
4X-RAY DIFFRACTION2ALLBBB201
5X-RAY DIFFRACTION2ALLAAA201
6X-RAY DIFFRACTION2ALLBBB202 - 203
7X-RAY DIFFRACTION2ALLBBB301 - 455

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