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- PDB-6ip9: Crystal Structure of Lanthanum ion (La3+) bound bovine alpha-lact... -

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Basic information

Entry
Database: PDB / ID: 6ip9
TitleCrystal Structure of Lanthanum ion (La3+) bound bovine alpha-lactalbumin
ComponentsAlpha-lactalbumin
KeywordsMETAL BINDING PROTEIN / Lanthanum / bovine alpha-lactalbumin / HAMLET / BAMLET
Function / homology
Function and homology information


response to 11-deoxycorticosterone / response to dehydroepiandrosterone / lactose synthase activity / lactose biosynthetic process / response to progesterone / lysozyme activity / response to estradiol / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding ...response to 11-deoxycorticosterone / response to dehydroepiandrosterone / lactose synthase activity / lactose biosynthetic process / response to progesterone / lysozyme activity / response to estradiol / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding / : / identical protein binding
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
LANTHANUM (III) ION / Alpha-lactalbumin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPrakash, P. / Yarramala, S.D. / Rao, C.P. / Bhaumik, P.
Funding support India, 1items
OrganizationGrant numberCountry
BT/RLF/Re-entry/42/2011 India
CitationJournal: Sci Rep / Year: 2019
Title: Cytotoxicity of apo bovine alpha-lactalbumin complexed with La3+on cancer cells supported by its high resolution crystal structure.
Authors: Yarramala, D.S. / Prakash, P. / Ranade, D.S. / Doshi, S. / Kulkarni, P.P. / Bhaumik, P. / Rao, C.P.
History
DepositionNov 2, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 20, 2019ID: 5X84
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)14,5294
Polymers14,2021
Non-polymers3273
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area6470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.450, 47.450, 89.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

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Components

#1: Protein Alpha-lactalbumin / Lactose synthase B protein


Mass: 14202.048 Da / Num. of mol.: 1 / Fragment: UNP residues 20-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: LALBA / Production host: Enterobacteria phage L1 (virus) / References: UniProt: P00711
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-LA / LANTHANUM (III) ION


Mass: 138.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: La
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M Tris-HCl at pH 6.0, 2M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 10499 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.066 / Net I/σ(I): 25.6
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.48 / Num. unique obs: 1496 / CC1/2: 0.81 / Rrim(I) all: 0.53 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→19.72 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.369 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.132 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21583 524 5 %RANDOM
Rwork0.19662 ---
obs0.19763 9963 99.84 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 31.027 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.85→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 12 62 1041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131013
X-RAY DIFFRACTIONr_bond_other_d0.0020.017886
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.631377
X-RAY DIFFRACTIONr_angle_other_deg1.3091.592082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31726.34652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72215181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.489151
X-RAY DIFFRACTIONr_chiral_restr0.0720.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021121
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02190
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1911.486483
X-RAY DIFFRACTIONr_mcbond_other1.191.483482
X-RAY DIFFRACTIONr_mcangle_it1.8492.223603
X-RAY DIFFRACTIONr_mcangle_other1.8492.226604
X-RAY DIFFRACTIONr_scbond_it1.6361.659528
X-RAY DIFFRACTIONr_scbond_other1.6361.664529
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4592.427772
X-RAY DIFFRACTIONr_long_range_B_refined4.80918.0551185
X-RAY DIFFRACTIONr_long_range_B_other4.77217.8541178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 38 -
Rwork0.264 737 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: 10.27 Å / Origin y: -14.946 Å / Origin z: -6.394 Å
111213212223313233
T0.0574 Å2-0.0016 Å20.0103 Å2-0.0433 Å20.0032 Å2--0.0204 Å2
L9.146 °23.0712 °2-1.6338 °2-2.2583 °2-0.2488 °2--3.1424 °2
S0.4045 Å °0.1133 Å °-0.0687 Å °0.1807 Å °-0.1879 Å °-0.0542 Å °-0.3064 Å °-0.0646 Å °-0.2166 Å °

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