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- PDB-1b9o: HUMAN ALPHA-LACTALBUMIN, LOW TEMPERATURE FORM -

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Basic information

Entry
Database: PDB / ID: 1b9o
TitleHUMAN ALPHA-LACTALBUMIN, LOW TEMPERATURE FORM
ComponentsPROTEIN (ALPHA-LACTALBUMIN)
KeywordsCALCIUM-BINDING PROTEIN / HIGH RESOLUTION
Function / homology
Function and homology information


Lactose synthesis / lactose synthase activity / lactose biosynthetic process / Golgi lumen / cell-cell signaling / lysozyme activity / defense response to bacterium / Golgi membrane / apoptotic process / calcium ion binding ...Lactose synthesis / lactose synthase activity / lactose biosynthetic process / Golgi lumen / cell-cell signaling / lysozyme activity / 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 / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsHarata, K. / Abe, Y. / Muraki, M.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystallographic evaluation of internal motion of human alpha-lactalbumin refined by full-matrix least-squares method.
Authors: Harata, K. / Abe, Y. / Muraki, M.
History
DepositionFeb 14, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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

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Assembly

Deposited unit
A: PROTEIN (ALPHA-LACTALBUMIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1342
Polymers14,0941
Non-polymers401
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.190, 49.550, 64.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein PROTEIN (ALPHA-LACTALBUMIN)


Mass: 14094.112 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00709
#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 / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.31 %
Crystal growpH: 4.2 / Details: pH 4.2
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 %protein11
22 M11(ND4)2SO4

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS / Detector: CCD
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.15→23.1 Å / Num. all: 37696 / Num. obs: 37696 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10
Reflection shellResolution: 1.15→1.17 Å / Rmerge(I) obs: 0.192 / % possible all: 96
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

Software
NameClassification
MADNESSdata collection
MERGEFdata reduction
X-PLORmodel building
SHELXLrefinement
MADNESSdata reduction
MERGEFdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→23.1 Å / Num. parameters: 10757 / Num. restraintsaints: 13066 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.162 3769 10 %EVERY 10TH REFLECTION
all0.119 37696 --
obs0.122 37696 98.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 11
Refinement stepCycle: LAST / Resolution: 1.15→23.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 1 164 1195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.014
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.1
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.016
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0.152

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