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- PDB-3kza: Crystal structure of Gyuba, a patched chimera of b-lactglobulin -

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Basic information

Entry
Database: PDB / ID: 3kza
TitleCrystal structure of Gyuba, a patched chimera of b-lactglobulin
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / artificial protein / chimera protein / Disulfide bond / Milk protein / Retinol-binding / Secreted / Transport
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 / 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
Beta-lactoglobulin / Beta-lactoglobulin-1
Similarity search - Component
Biological speciesEquus caballus (horse)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTsuge, H. / Ohtomo, H. / Utsunomiya, H. / Konuma, T. / Ikeguchi, M.
CitationJournal: Protein Sci. / Year: 2011
Title: Structure and stability of Gyuba, a patched chimera of b-lactoglobulin
Authors: Ohtomo, H. / Konuma, T. / Utsunoiya, H. / Tsuge, H. / Ikeguchi, M.
History
DepositionDec 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 9, 2011Group: Database references
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactoglobulin
B: Beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)36,6222
Polymers36,6222
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)18,3111
Polymers18,3111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)18,3111
Polymers18,3111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.925, 68.925, 151.616
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Beta-lactoglobulin / / Beta-LG-1 / Beta-lactoglobulin I / BLGI


Mass: 18310.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: AN ARTIFICIAL CHIMERA PROTEIN OF BOS-TAURAS AND EQUINE B-LACTOGLOBULIN. THE RESIDUES 1-16, 28-41, 50, 51, 63-65, 74-49, 87, 88, 96-101, 109-116, 125-129, 139-144, 154-162 ARE FROM EQUINE, ...Details: AN ARTIFICIAL CHIMERA PROTEIN OF BOS-TAURAS AND EQUINE B-LACTOGLOBULIN. THE RESIDUES 1-16, 28-41, 50, 51, 63-65, 74-49, 87, 88, 96-101, 109-116, 125-129, 139-144, 154-162 ARE FROM EQUINE, THE RESIDUES 17-27, 42-49, 52-62, 66-73, 80-86, 89-95, 102-108, 117-124, 130-138, 145-153 ARE FROM BOS-TAURAS.
Source: (gene. exp.) Equus caballus (horse), (gene. exp.) Bos taurus (cattle)
Gene: LGB1 / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P02758, UniProt: P02754
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS IS AN ARTIFICIAL CHIMERA PROTEIN OF BOS-TAURAS AND EQUINE B-LACTOGLOBULIN.

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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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→59.66 Å / Num. obs: 27566 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.9 % / Rsym value: 0.066 / Net I/σ(I): 15.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 9.6 % / Num. unique all: 2741 / Rsym value: 0.314 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→59.66 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.16 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28491 1383 5 %RANDOM
Rwork0.2346 ---
obs0.23718 26122 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.665 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20.56 Å20 Å2
2--1.12 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2→59.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 0 240 2576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222376
X-RAY DIFFRACTIONr_angle_refined_deg1.992.0053222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7395294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74826.538104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.72215442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.135158
X-RAY DIFFRACTIONr_chiral_restr0.1740.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021752
X-RAY DIFFRACTIONr_nbd_refined0.2440.21022
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21593
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2199
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.27
X-RAY DIFFRACTIONr_mcbond_it1.3971.51559
X-RAY DIFFRACTIONr_mcangle_it2.23722424
X-RAY DIFFRACTIONr_scbond_it3.6923947
X-RAY DIFFRACTIONr_scangle_it5.4884.5798
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 99 -
Rwork0.244 1915 -
obs--98.44 %

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