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- PDB-1f6r: CRYSTAL STRUCTURE OF APO-BOVINE ALPHA-LACTALBUMIN -

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Basic information

Entry
Database: PDB / ID: 1f6r
TitleCRYSTAL STRUCTURE OF APO-BOVINE ALPHA-LACTALBUMIN
ComponentsALPHA-LACTALBUMIN
KeywordsMETAL BINDING PROTEIN / Calcium binding protein
Function / homology
Function and homology information


response to dehydroepiandrosterone / response to 11-deoxycorticosterone / lactose synthase activity / lactose biosynthetic process / response to progesterone / response to estradiol / lysozyme activity / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding ...response to dehydroepiandrosterone / response to 11-deoxycorticosterone / lactose synthase activity / lactose biosynthetic process / response to progesterone / response to estradiol / lysozyme activity / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding / extracellular space / identical protein binding
Similarity search - Function
Lactalbumin / Lysozyme - #10 / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lactalbumin / Lysozyme - #10 / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsChrysina, E.D. / Brew, K. / Acharya, K.R.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Crystal structures of apo- and holo-bovine alpha-lactalbumin at 2. 2-A resolution reveal an effect of calcium on inter-lobe interactions.
Authors: Chrysina, E.D. / Brew, K. / Acharya, K.R.
#1: Journal: Biochemistry / Year: 1998
Title: Structural Evidence for the Presence of a Secondary Calcium Binding Site in Human Alpha-Lactalbumin
Authors: Chandra, N. / Brew, K. / Acharya, K.R.
#2: Journal: Structure / Year: 1996
Title: Crystal Structures of Guinea-pig, Goat and Bovine Alpha-Lactalbumin Highlight the Enhanced Conformational Flexibility of Regions that are Significant for its Action in Lactose Synthase
Authors: Pike, A.C. / Brew, K. / Acharya, K.R.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Crystal Structure of Human Alpha-Lactalbumin at 1.7 A Resolution
Authors: Acharya, K.R. / Ren, J.S. / Stuart, D.I. / Phillips, D.C. / Fenna, R.E.
#4: Journal: J.Mol.Biol. / Year: 1989
Title: Refined Structure of Baboon Alpha-Lactalbumin at 1.7 A Resolution. Comparison with C-type Lysozyme
Authors: Acharya, K.R. / Stuart, D.I. / Walker, N.P. / Lewis, M. / Phillips, D.C.
#5: Journal: Nature / Year: 1986
Title: Alpha-Lactalbumin Possesses a Novel Calcium-Binding Loop
Authors: Stuart, D.I. / Acharya, K.R. / Walker, N.P. / Smith, S.G. / Lewis, M. / Phillips, D.C.
History
DepositionJun 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-LACTALBUMIN
B: ALPHA-LACTALBUMIN
C: ALPHA-LACTALBUMIN
D: ALPHA-LACTALBUMIN
E: ALPHA-LACTALBUMIN
F: ALPHA-LACTALBUMIN


Theoretical massNumber of molelcules
Total (without water)85,2126
Polymers85,2126
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.568, 119.568, 152.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
ALPHA-LACTALBUMIN


Mass: 14202.048 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00711
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulfate, Tris/HCl buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
22.0 Mammonium sulfate1reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 26, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 57273 / Num. obs: 561254 / % possible obs: 99.3 % / Redundancy: 9.8 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.633 / Num. unique all: 5653 / % possible all: 99.5
Reflection
*PLUS
Num. obs: 57273 / Num. measured all: 561254
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementResolution: 2.2→40 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2839 5 %RANDOM
Rwork0.191 ---
obs0.191 56422 99.4 %-
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5839 0 0 167 6006
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d25.9
X-RAY DIFFRACTIONx_improper_angle_d0.81
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 489 5.3 %
Rwork0.294 8770 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramtophcsdx.pro
X-RAY DIFFRACTION2param.watertop.water
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.81

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