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- PDB-1beb: BOVINE BETA-LACTOGLOBULIN, LATTICE X -

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Basic information

Entry
Database: PDB / ID: 1beb
TitleBOVINE BETA-LACTOGLOBULIN, LATTICE X
ComponentsBETA-LACTOGLOBULIN
KeywordsLIPOCALIN / MILK WHEY PROTEIN / BOVINE / RETINOL-BINDING
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBrownlow, S. / Morais-Cabral, J.H. / Sawyer, L.
CitationJournal: Structure / Year: 1997
Title: Bovine beta-lactoglobulin at 1.8 A resolution--still an enigmatic lipocalin.
Authors: Brownlow, S. / Morais Cabral, J.H. / Cooper, R. / Flower, D.R. / Yewdall, S.J. / Polikarpov, I. / North, A.C. / Sawyer, L.
History
DepositionDec 20, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-LACTOGLOBULIN
B: BETA-LACTOGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7553
Polymers36,6582
Non-polymers961
Water3,549197
1
A: BETA-LACTOGLOBULIN


Theoretical massNumber of molelcules
Total (without water)18,3291
Polymers18,3291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-LACTOGLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4252
Polymers18,3291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.800, 49.500, 56.600
Angle α, β, γ (deg.)123.40, 97.30, 103.70
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.14058, -0.80081, -0.58218), (-0.81017, -0.24494, 0.53256), (-0.56908, 0.54654, -0.61436)
Vector: 0.07884, -0.1288, 0.00728)

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Components

#1: Protein BETA-LACTOGLOBULIN


Mass: 18329.229 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PROTEIN PURCHASED FROM SIGMA CHEMICALS / Source: (natural) Bos taurus (domestic cattle) / Secretion: MILK / Variant: MIXTURE OF GENETIC VARIANTS A AND B / References: UniProt: P02754
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 42 %
Crystal growMethod: batch method / pH: 6.5
Details: 25MG/ML PROTEIN WAS DISSOLVED IN 0.1M SODIUM/ POTASSIUM PHOSPHATE BUFFER (PH 7.0) AND CRYSTALLIZED BY THE BATCH METHOD FROM 2M AMMONIUM SULFATE (PH 6.5) AND 0.4M SODIUM/POTASSIUM PHOSPHATE ...Details: 25MG/ML PROTEIN WAS DISSOLVED IN 0.1M SODIUM/ POTASSIUM PHOSPHATE BUFFER (PH 7.0) AND CRYSTALLIZED BY THE BATCH METHOD FROM 2M AMMONIUM SULFATE (PH 6.5) AND 0.4M SODIUM/POTASSIUM PHOSPHATE BUFFER (PH 7.6)., batch method
PH range: 6.5-7.6
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122.7 mg/mlprotein11
20.42 Msodium potassium phosphate11
32 Mammonium sulfate11adjuste to pH6.5 with 0.88M ammonia
50.001 %(w/v)sodium azide11
4water110.25ml

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Sep 1, 1988 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 25155 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.1 / Net I/σ(I): 5
Reflection shellResolution: 1.8→1.96 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 3 / Rsym value: 0.1 / % possible all: 78

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Processing

Software
NameVersionClassification
XDSdata scaling
ROTAVATAdata reduction
Agrovatadata reduction
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: B-LG LATTICE Z - SOLVED BY MIR

Resolution: 1.8→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1256 5 %RANDOM
Rwork0.181 ---
obs0.181 25135 96 %-
Displacement parametersBiso mean: 25.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2473 0 0 197 2670
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.545
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.08
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.366
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.2
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2
Refine LS restraints NCSNCS model details: UNRESTRAINED AT END
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.33 874 3.478 %
Rwork0.3 16053 -
obs--67 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION4PARAM.SO4TOP.SO4
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.084
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.366
LS refinement shell
*PLUS
Rfactor Rwork: 0.3

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