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- PDB-1hmk: RECOMBINANT GOAT ALPHA-LACTALBUMIN -

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Basic information

Entry
Database: PDB / ID: 1hmk
TitleRECOMBINANT GOAT ALPHA-LACTALBUMIN
ComponentsPROTEIN (ALPHA-LACTALBUMIN)
KeywordsTRANSFERASE / LACTOSE SYNTHASE COMPONENT / CALCIUM BINDING METALLOPROTEIN / GLYCOPROTEIN
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 / protein-containing complex / 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 speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHorii, K. / Matsushima, M. / Tsumoto, K. / Kumagai, I.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Effect of the extra n-terminal methionine residue on the stability and folding of recombinant alpha-lactalbumin expressed in Escherichia coli.
Authors: Chaudhuri, T.K. / Horii, K. / Yoda, T. / Arai, M. / Nagata, S. / Terada, T.P. / Uchiyama, H. / Ikura, T. / Tsumoto, K. / Kataoka, H. / Matsushima, M. / Kuwajima, K. / Kumagai, I.
#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: Protein Eng. / Year: 1995
Title: Effects of Amino Acid Substitutions in the Hydrophobic Core of Alpha-Lactalbumin on the Stability of the Molten Globule State
Authors: Uchiyama, H. / Perez-Prat, E.M. / Watanabe, K. / Kumagai, I. / Kuwajima, K.
History
DepositionNov 26, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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_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_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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Nov 20, 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: PROTEIN (ALPHA-LACTALBUMIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3822
Polymers14,3421
Non-polymers401
Water1,44180
1
A: PROTEIN (ALPHA-LACTALBUMIN)
hetero molecules

A: PROTEIN (ALPHA-LACTALBUMIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7654
Polymers28,6852
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Unit cell
Length a, b, c (Å)44.850, 88.940, 32.160
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 PROTEIN (ALPHA-LACTALBUMIN)


Mass: 14342.254 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capra hircus (goat) / Gene: A CLONED GENE OF GOAT LACTA / Plasmid: PET-PUT7LA / Species (production host): Escherichia coli / Gene (production host): A CLONED GENE OF GOAT CDNA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00712, lactose synthase
#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.: 80 / 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: 2.2 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 293 K / pH: 6 / Details: pH 6.0, temperature 293K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
21.0 mM1reservoirCaCl2
316-20 %PEG80001reservoir
40.05 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 282 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 12533 / % possible obs: 92.5 % / Observed criterion σ(I): 0.0001 / Redundancy: 5.1 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.309 / % possible all: 94.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BABOON ALPHA-LACTALBUMIN

Resolution: 2→8 Å / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE SIDE CHAIN OF GLN 2, WHICH IS CLOSE TO A ROTAION AXIS IN THE CRYSTAL, IS DISORDERED. THE ELECTRON DENSITY IS WELL DEFINED. THE C-TERMINAL TRIPEPTIDE (GLU 121 - LEU 123) IS POORLY DEFINED ...Details: THE SIDE CHAIN OF GLN 2, WHICH IS CLOSE TO A ROTAION AXIS IN THE CRYSTAL, IS DISORDERED. THE ELECTRON DENSITY IS WELL DEFINED. THE C-TERMINAL TRIPEPTIDE (GLU 121 - LEU 123) IS POORLY DEFINED IN THE ELECTRON DENSITY AND THEREFORE THESE RESIDUES HAVE NOT BEEN INCLUDED IN THE FINAL MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 -10 %RANDOM
Rwork0.198 ---
obs0.198 64394 92.5 %-
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 1 80 1057
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.22
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.46
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.61
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
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.191 / Rfactor Rfree: 0.278
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.554
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.46
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.61

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