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- PDB-1alc: REFINED STRUCTURE OF BABOON ALPHA-LACTALBUMIN AT 1.7 ANGSTROMS RE... -

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Entry
Database: PDB / ID: 1alc
TitleREFINED STRUCTURE OF BABOON ALPHA-LACTALBUMIN AT 1.7 ANGSTROMS RESOLUTION. COMPARISON WITH C-TYPE LYSOZYME
ComponentsALPHA-LACTALBUMIN
KeywordsCALCIUM BINDING PROTEIN
Function / homology
Function and homology information


lactose synthase activity / lactose biosynthetic process / lysozyme activity / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding / extracellular region
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 speciesPapio cynocephalus (Yellow baboon)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsAcharya, K.R. / Stuart, D.I. / Phillips, D.C.
Citation
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.
#1: Journal: Biochem.J. / Year: 1987
Title: Crystallographic Analysis of the Three-Dimensional Structure of Baboon Alpha-Lactalbumin at Low Resolution. Homology with Lysozyme
Authors: Smith, S.G. / Lewis, M. / Aschaffenburg, R. / Fenna, R.E. / Wilson, I.A. / Sundaralingam, M. / Stuart, D.I. / Phillips, D.C.
#2: Journal: Nature / Year: 1986
Title: Alpha-Lactalbumin Possesses a Novel Calcium Binding Loop
Authors: Stuart, D.I. / Acharya, K.R. / Walker, N.P.C. / Smith, S.G. / Lewis, M. / Phillips, D.C.
#3: Journal: J.Mol.Biol. / Year: 1979
Title: Crystallography of Alpha-Lactalbumin. III. Crystals of Baboon Milk Alpha-Lactalbumin
Authors: Aschaffenburg, R. / Fenna, R.E. / Phillips, D.C. / Smith, S.G. / Buss, D.H. / Jeness, R. / Thompson, M.P.
History
DepositionAug 14, 1989Processing site: BNL
Revision 1.0Oct 15, 1989Provider: 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_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_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.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_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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-LACTALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2292
Polymers14,1891
Non-polymers401
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.500, 69.100, 46.100
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: 14189.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Papio cynocephalus (Yellow baboon) / References: UniProt: P12065
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.26 %
Crystal grow
*PLUS
pH: 6.8 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
145 %satammonium sulfate11
20.2 Mphosphate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 9999 Å / Num. all: 13025 / Num. obs: 12400 / Observed criterion σ(F): 2 / Num. measured all: 10275
Reflection shell
*PLUS
Highest resolution: 1.7 Å

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.7 Å /
RfactorNum. reflection
all0.22 -
obs-10275
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 1 150 1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.035
X-RAY DIFFRACTIONp_angle_d0.0270.045
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0210.045
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it31.65
X-RAY DIFFRACTIONp_mcangle_it26.56
X-RAY DIFFRACTIONp_scbond_it42.96
X-RAY DIFFRACTIONp_scangle_it33.28
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.2290.25
X-RAY DIFFRACTIONp_singtor_nbd0.1110.9
X-RAY DIFFRACTIONp_multtor_nbd0.5230.9
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3480.9
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.76
X-RAY DIFFRACTIONp_staggered_tor25.225
X-RAY DIFFRACTIONp_orthonormal_tor27.625
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.22 / Highest resolution: 1.7 Å / Lowest resolution: 9999 Å / Num. reflection obs: 10275
Solvent computation
*PLUS
Displacement parameters
*PLUS

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