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Basic information

Entry
Database: PDB / ID: 1hfz
TitleALPHA-LACTALBUMIN
ComponentsALPHA-LACTALBUMIN
KeywordsGLYCOPROTEIN / LACTOSE SYNTHASE COMPONENT / CALCIUM BINDING METALLOPROTEIN / LACTOSE
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: 2.3 Å
AuthorsPike, A.C.W. / Brew, K. / Acharya, K.R.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Study by Mutagenesis of the Roles of Two Aromatic Clusters of Alpha-Lactalbumin in Aspects of its Action in the Lactose Synthase System
Authors: Grobler, J.A. / Wang, M. / Pike, A.C. / Brew, K.
#2: 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.
#3: 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.
History
DepositionJun 13, 1996Processing site: BNL
Revision 1.0Jul 29, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_asym_id / _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_asym_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_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: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-LACTALBUMIN
B: ALPHA-LACTALBUMIN
C: ALPHA-LACTALBUMIN
D: ALPHA-LACTALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3658
Polymers57,2054
Non-polymers1604
Water1,08160
1
A: ALPHA-LACTALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3412
Polymers14,3011
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ALPHA-LACTALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3412
Polymers14,3011
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ALPHA-LACTALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3412
Polymers14,3011
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ALPHA-LACTALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3412
Polymers14,3011
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.620, 60.130, 77.180
Angle α, β, γ (deg.)90.00, 96.85, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.97009, -0.00717, 0.24264), (-0.00708, -0.99997, -0.00124), (0.24265, -0.00052, -0.97011)-4.62755, 25.96332, 38.36529
2given(-0.61141, -0.67951, -0.4055), (0.59176, -0.05242, -0.80441), (0.52535, -0.73179, 0.43416)47.31558, 4.81523, -4.94719
3given(-0.47677, -0.83759, -0.26671), (-0.57019, 0.06376, 0.81903), (-0.66901, 0.54257, -0.50799)41.91967, 21.05887, 40.44951
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO DIMERS (CHAINS A AND B AND CHAINS C AND D). THE ADDITIONAL N-TERMINAL METHIONINE OF EACH CHAIN, INTRODUCED BY THE CLONING PROCEDURE, HAS BEEN NUMBERED 1X SO THAT THE REMAINING RESIDUES (1 - 123) HAVE A NUMBERING SCHEME THAT IS IDENTICAL TO OTHER ALPHA-LACTALBUMIN STRUCTURES.

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Components

#1: Protein
ALPHA-LACTALBUMIN


Mass: 14301.180 Da / Num. of mol.: 4 / Mutation: INS(MET 1X), M90V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Description: T7 RNA POLYMERASE / Gene: BOVINE ALPHA-LACTALBUMIN CDNA / Plasmid: PET3A / Gene (production host): BOVINE ALPHA-LACTALBUMIN CDNA / Production host: Escherichia coli (E. coli) / References: UniProt: P00711, lactose synthase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 8

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.15 M1reservoirMgAc
320-25 %PEG40001reservoir
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 / Wavelength: 0.87, 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 24, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
20.951
ReflectionNum. obs: 18629 / % possible obs: 80 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.078
Reflection
*PLUS
Highest resolution: 2.3 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.3→8 Å / σ(F): 0
Details: CHAINS C AND D ARE GENERALLY POORLY DEFINED IN THE ELECTRON DENSITY DUE TO PACKING DISORDER WITHIN THE CRYSTAL. THIS IS REFLECTED IN THE RELATIVELY HIGH OVERALL TEMPERATURE FACTOR OBSERVED FOR THESE CHAINS.
RfactorNum. reflection
Rfree0.303 -
Rwork0.208 -
obs0.208 18605
Displacement parametersBiso mean: 48.39 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3958 0 4 60 4022
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.73
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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