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- PDB-1f6s: CRYSTAL STRUCTURE OF BOVINE ALPHA-LACTALBUMIN -

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Basic information

Entry
Database: PDB / ID: 1f6s
TitleCRYSTAL STRUCTURE OF BOVINE ALPHA-LACTALBUMIN
ComponentsALPHA-LACTALBUMIN
KeywordsMETAL BINDING PROTEIN / Calcium binding protein
Function / homology
Function and homology information


response to 11-deoxycorticosterone / response to dehydroepiandrosterone / lactose synthase activity / lactose biosynthetic process / response to progesterone / lysozyme activity / response to estradiol / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding ...response to 11-deoxycorticosterone / response to dehydroepiandrosterone / lactose synthase activity / lactose biosynthetic process / response to progesterone / lysozyme activity / response to estradiol / 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 (domestic 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
Revision 1.3Dec 18, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,45312
Polymers85,2126
Non-polymers2406
Water1,60389
1
A: ALPHA-LACTALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2422
Polymers14,2021
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-LACTALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2422
Polymers14,2021
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ALPHA-LACTALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2422
Polymers14,2021
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ALPHA-LACTALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2422
Polymers14,2021
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ALPHA-LACTALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2422
Polymers14,2021
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ALPHA-LACTALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2422
Polymers14,2021
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.045, 104.650, 117.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 (domestic cattle) / References: UniProt: P00711
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.6 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Polyethylene glycol, Potassium dihydrogen orthophosphate, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %PEG80001reservoir
20.05 Mpotassium dihydrogen orthophosphate1reservoir
320 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.847
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.847 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 45363 / Num. obs: 371734 / % possible obs: 99.2 % / Redundancy: 8.2 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.517 / Num. unique all: 4182 / % possible all: 99.2
Reflection
*PLUS
Num. obs: 45363 / Num. measured all: 371734
Reflection shell
*PLUS
% possible obs: 99.2 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.2→29.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1132224.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4581 10.1 %RANDOM
Rwork0.216 ---
obs0.216 45348 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.59 Å2 / ksol: 0.416 e/Å3
Displacement parametersBiso mean: 49.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.21 Å20 Å20 Å2
2--0.12 Å20 Å2
3----4.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5850 0 6 89 5945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 740 10.2 %
Rwork0.299 6536 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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