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- PDB-1a4v: ALPHA-LACTALBUMIN -

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Basic information

Entry
Database: PDB / ID: 1a4v
TitleALPHA-LACTALBUMIN
ComponentsALPHA-LACTALBUMIN
KeywordsLACTOSE SYNTHASE / CALCIUM BINDING / ALPHA-LACTALBUMIN
Function / homology
Function and homology information


Lactose synthesis / lactose synthase activity / lactose biosynthetic process / Golgi lumen / lysozyme activity / cell-cell signaling / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / Golgi membrane ...Lactose synthesis / lactose synthase activity / lactose biosynthetic process / Golgi lumen / lysozyme activity / cell-cell signaling / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / Golgi membrane / apoptotic process / calcium ion binding / signal transduction / protein-containing complex / extracellular space
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsChandra, N. / Acharya, K.R.
Citation
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.
#1: 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.
#2: 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.
#3: Journal: J.Biol.Chem. / Year: 1993
Title: Alpha-Lactalbumin Possesses a Distinct Zinc Binding Site
Authors: Ren, J. / Stuart, D.I. / Acharya, K.R.
#4: 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.
History
DepositionFeb 5, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1733
Polymers14,0931
Non-polymers802
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.470, 69.560, 45.960
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 / ALPHA-LA


Mass: 14093.128 Da / Num. of mol.: 1 / Fragment: CALCIUM-BINDING REGION / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
Cellular location: TRANS-GOLGI APPARATUS OF THE MAMMARY GLAND
Secretion: MILK / References: UniProt: P00709, lactose synthase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.99 Å3/Da / Density % sol: 38 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.1 MPIPES1drop
31.8 Mammonium sulfate1drop
4100 mM1dropCaCl2
52.0 Mammonium sulfate1reservoir
6100 mM1reservoirCaCl2
70.2 MPIPES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1992 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→8 Å / Num. obs: 9928 / % possible obs: 82 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 5.6 Å2 / Rsym value: 0.0699 / Net I/σ(I): 14.33
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 0.31 % / Mean I/σ(I) obs: 1.03 / Rsym value: 0.337 / % possible all: 64
Reflection
*PLUS
Num. measured all: 40180 / Rmerge(I) obs: 0.0699
Reflection shell
*PLUS
% possible obs: 64 % / Rmerge(I) obs: 0.018

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata scaling
X-PLOR3.1phasing
RefinementResolution: 1.8→8 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.263 424 5.4 %RANDOM
Rwork0.21 ---
obs0.21 8907 82 %-
Displacement parametersBiso mean: 16.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 2 321 1415
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.15
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.067 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.178 7 4.2 %
Rwork0.243 161 -
obs--15.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPOW.WATER
X-RAY DIFFRACTION2PARAM.WATERTOP.CAL
X-RAY DIFFRACTION3PARAM.CAL
X-RAY DIFFRACTION4TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.15

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