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- PDB-3ph5: Bovine beta lactoglobulin crystallized through ligandation of ytt... -

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Basic information

Entry
Database: PDB / ID: 3ph5
TitleBovine beta lactoglobulin crystallized through ligandation of yttrium cations
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN
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
YTTRIUM (III) ION / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsZocher, G. / Stehle, T.
CitationJournal: J.Appl.Crystallogr. / Year: 2011
Title: Novel Approach to Protein Crystallization through Ligandation of Yttrium Cations
Authors: Zhang, F. / Zocher, G. / Sauter, A. / Stehle, T. / Schreiber, F.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,8038
Polymers36,3762
Non-polymers4276
Water70339
1
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4375
Polymers18,1881
Non-polymers2494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3663
Polymers18,1881
Non-polymers1782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.800, 63.570, 134.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 18188.018 Da / Num. of mol.: 2 / Fragment: unp residues 18-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P02754
#2: Chemical
ChemComp-YT3 / YTTRIUM (III) ION / Yttrium


Mass: 88.906 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Y
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 277 K / Method: batch crystallization / pH: 7
Details: Crystallized in presents of 3.0 mM yttrium(III) chlorid, pH 7, Batch Crystallization, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.5418
SYNCHROTRONSLS X06DA21.8233
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATEJul 2, 2009
MARMOSAIC 225 mm CCD2CCDJul 13, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1copperSINGLE WAVELENGTHMx-ray1
2DCCMSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.82331
ReflectionResolution: 2.4→20 Å / Num. all: 14221 / Num. obs: 14221 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.068 / Net I/σ(I): 19.1
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 3 / Num. unique all: 1930 / Rsym value: 0.523 / % possible all: 99.9

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Processing

Software
NameVersionClassification
RAMDAQdata collection
SHARPphasing
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.59 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.916 / SU B: 20.819 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26314 712 5 %RANDOM
Rwork0.2223 ---
obs0.22432 13510 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.233 Å2
Baniso -1Baniso -2Baniso -3
1-5.94 Å2-0 Å2-0 Å2
2---3.82 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 6 39 2491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222492
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.9933386
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1025313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72926.538104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23415453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.95156
X-RAY DIFFRACTIONr_chiral_restr0.0640.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211834
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.53541583
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88842552
X-RAY DIFFRACTIONr_scbond_it0.855909
X-RAY DIFFRACTIONr_scangle_it1.195834
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 50 -
Rwork0.31 949 -
obs--100 %
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)
12.3605-0.14351.41785.70330.83496.72480.03460.1489-0.2325-0.3374-0.013-0.23070.35310.0529-0.02160.04890.01150.02110.0655-0.02410.0476-0.4725-2.615-24.0739
22.65031.68611.66665.2037-0.11866.84490.1926-0.1227-0.06690.8738-0.0549-0.32560.00620.0669-0.13770.15790.0127-0.06950.0707-0.01470.16367.81012.28925.2634
31.19520.00562.18130.9565-1.40336.14590.17250.1728-0.32850.1110.2222-0.03610.265-0.0409-0.39470.31760.05450.14290.1484-0.16380.40362.5009-1.6154-20.365
40.29350.69490.53691.97450.2984.1139-0.0450.0022-0.0762-0.19210.0414-0.1762-0.0371-0.18180.00350.04030.04210.01770.0989-0.00280.23651.97351.4686-15.1423
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 178
2X-RAY DIFFRACTION2B23 - 178
3X-RAY DIFFRACTION3A1 - 6
4X-RAY DIFFRACTION3B3 - 4
5X-RAY DIFFRACTION4A3 - 16
6X-RAY DIFFRACTION4A179 - 193
7X-RAY DIFFRACTION4B15
8X-RAY DIFFRACTION4B179 - 192

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