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- PDB-4lzu: Bovine beta-lactoglobulin crystallized in the presence of 2 mM zi... -

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Basic information

Entry
Database: PDB / ID: 4lzu
TitleBovine beta-lactoglobulin crystallized in the presence of 2 mM zinc chloride
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOelker, M. / Zocher, G. / Stehle, T.
CitationJournal: To be Published
Title: Non-Classical Pathways of Protein Crystallization in the Presence of Multivalent Metal Ions
Authors: Sauter, A. / Oelker, M. / Zocher, G. / Zhang, F. / Stehle, T. / Schreiber, F.
History
DepositionAug 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4323
Polymers18,3011
Non-polymers1312
Water724
1
A: Beta-lactoglobulin
hetero molecules

A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8646
Polymers36,6022
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area1360 Å2
ΔGint-91 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.830, 92.830, 42.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18301.174 Da / Num. of mol.: 1 / Fragment: UNP residues 17-178 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02754
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 277 K / Method: batch / pH: 6
Details: 2 mM zinc chloride, pH 6.0, BATCH, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 25, 2011
RadiationMonochromator: Bartels Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→19.73 Å / Num. all: 8425 / Num. obs: 8425 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Net I/σ(I): 29.62
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 3.05 / % possible all: 99.5

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
REFMAC5.8.0025refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PH5

3ph5


Resolution: 2.4→19.73 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 16.857 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23147 1011 12 %RANDOM
Rwork0.19597 ---
obs0.20016 7414 99.7 %-
all-7414 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.463 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20.67 Å2-0 Å2
2--1.35 Å2-0 Å2
3----4.37 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1261 0 2 4 1267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191287
X-RAY DIFFRACTIONr_bond_other_d0.0010.021263
X-RAY DIFFRACTIONr_angle_refined_deg0.8981.9941740
X-RAY DIFFRACTIONr_angle_other_deg0.66432931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4725159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02526.66754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41415246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.86153
X-RAY DIFFRACTIONr_chiral_restr0.0550.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
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_it2.10510.926639
X-RAY DIFFRACTIONr_mcbond_other2.10210.925638
X-RAY DIFFRACTIONr_mcangle_it3.12214.332797
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.75711.565648
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.60943.91805
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 74 -
Rwork0.279 548 -
obs--99.84 %
Refinement TLS params.Method: refined / Origin x: 59.3399 Å / Origin y: -15.1155 Å / Origin z: 2.6126 Å
111213212223313233
T0.032 Å2-0.0248 Å2-0.0152 Å2-0.0219 Å20.0036 Å2--0.0326 Å2
L2.1872 °2-0.2786 °20.4947 °2-6.6598 °21.7369 °2--5.1792 °2
S0.0345 Å °-0.0288 Å °-0.0277 Å °0.0936 Å °0.0544 Å °-0.4395 Å °0.0433 Å °-0.027 Å °-0.0889 Å °

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