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- PDB-1fkv: RECOMBINANT GOAT ALPHA-LACTALBUMIN T29I -

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Basic information

Entry
Database: PDB / ID: 1fkv
TitleRECOMBINANT GOAT ALPHA-LACTALBUMIN T29I
ComponentsALPHA-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 / Resolution: 2 Å
AuthorsHorii, K. / Matsushima, M. / Tsumoto, K. / Kumagai, I.
Citation
Journal: Proteins / Year: 2001
Title: Contribution of Thr29 to the thermodynamic stability of goat alpha-lactalbumin as determined by experimental and theoretical approaches.
Authors: Horii, K. / Saito, M. / Yoda, T. / Tsumoto, K. / Matsushima, M. / Kuwajima, K. / Kumagai, I.
#1: 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.
History
DepositionAug 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_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

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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)14,3942
Polymers14,3541
Non-polymers401
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.800, 88.740, 32.380
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 / LACTOSE SYNTHASE B PROTEIN


Mass: 14354.307 Da / Num. of mol.: 1 / Fragment: B-HELIX / 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-T29I / 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.: 71 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, calcium chloride, potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130-40 mg/mlprotein1drop
21 mM1dropCaCl2
325 %PEG40001reservoir
40.2 Mammonium sulfate1reservoir
50.05 Mpotassium phosphate1reservoirpH5.5
61 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 282.5 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Sep 5, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 9147 / Num. obs: 8712 / % possible obs: 95.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.218 / % possible all: 95.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The C-terminal tripeptide (Glu121-Leu123) is poorly defined in the electron density and therefore these residues have not been included in the final model.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 862 -Random
Rwork0.193 ---
all-8129 --
obs-7267 93.3 %-
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 1 71 1049
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.208
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS

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