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- PDB-7evq: Crystal structure of C-terminal half of lactoferrin obtained by l... -

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Basic information

Entry
Database: PDB / ID: 7evq
TitleCrystal structure of C-terminal half of lactoferrin obtained by limited proteolysis using pepsin at 2.6 A resolution
ComponentsLactotransferrin
KeywordsIRON-BINDING PROTEIN / lactoferrin
Function / homology
Function and homology information


Metal sequestration by antimicrobial proteins / Antimicrobial peptides / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of osteoclast development / antifungal humoral response / specific granule / negative regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of chondrocyte proliferation ...Metal sequestration by antimicrobial proteins / Antimicrobial peptides / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of osteoclast development / antifungal humoral response / specific granule / negative regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of chondrocyte proliferation / regulation of tumor necrosis factor production / bone morphogenesis / Neutrophil degranulation / positive regulation of osteoblast proliferation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cysteine-type endopeptidase inhibitor activity / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / innate immune response in mucosa / iron ion transport / recycling endosome / antibacterial humoral response / early endosome / iron ion binding / signaling receptor binding / serine-type endopeptidase activity / negative regulation of apoptotic process / proteolysis / extracellular space / plasma membrane
Similarity search - Function
Lactotransferrin / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
BICARBONATE ION / : / Lactotransferrin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsViswanathan, V. / Singh, J. / Sharma, P. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)PDF/2018/000008 India
CitationJournal: To Be Published
Title: Crystal structure of C-terminal half of lactoferrin obtained by limited proteolysis using pepsin at 2.6 A resolution
Authors: Viswanathan, V. / Singh, J. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionMay 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactotransferrin
B: Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,10813
Polymers76,0242
Non-polymers3,08411
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint20 kcal/mol
Surface area30450 Å2
Unit cell
Length a, b, c (Å)153.246, 81.690, 110.227
Angle α, β, γ (deg.)90.000, 129.907, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-847-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 342 through 689 or resid 702 through 709))
d_2ens_1(chain "B" and (resid 342 through 689 or resid 708 through 703))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1TYRARGA1 - 348
d_12ens_1NAGNAGF
d_13ens_1BMABMAG
d_14ens_1NAGNAGH
d_15ens_1NAGNAGI
d_16ens_1BMABMAJ
d_21ens_1TYRARGA1 - 348
d_22ens_1NAGNAGF
d_23ens_1BMABMAG
d_24ens_1NAGNAGH
d_25ens_1NAGNAGI
d_26ens_1BMABMAJ

NCS oper: (Code: givenMatrix: (0.192071926117, -0.0369469481605, -0.980685116752), (-0.0425013599465, 0.998040348997, -0.0459248971302), (0.980460100973, 0.0505013345897, 0.190125236631)Vector: 75. ...NCS oper: (Code: given
Matrix: (0.192071926117, -0.0369469481605, -0.980685116752), (-0.0425013599465, 0.998040348997, -0.0459248971302), (0.980460100973, 0.0505013345897, 0.190125236631)
Vector: 75.5356251445, 42.9483687576, -8.34523020996)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lactotransferrin / Lactoferrin


Mass: 38011.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: P24627, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Sugars , 2 types, 6 molecules

#2: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 86 molecules

#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.48 Å3/Da / Density % sol: 64.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Magnesium Acetate 20%, PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.6→45.12 Å / Num. obs: 41125 / % possible obs: 64.8 % / Redundancy: 3 % / Biso Wilson estimate: 43.83 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.039 / Rrim(I) all: 0.078 / Net I/σ(I): 0.97
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1136 / CC1/2: 0.84 / Rpim(I) all: 0.26 / Rrim(I) all: 0.48 / % possible all: 22.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BFL

1bfl
PDB Unreleased entry


Resolution: 2.6→45.12 Å / SU ML: 0.4187 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.9683
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2841 2005 4.88 %
Rwork0.2269 39120 -
obs0.2296 41125 65.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.46 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5314 0 198 81 5593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00965607
X-RAY DIFFRACTIONf_angle_d1.4187596
X-RAY DIFFRACTIONf_chiral_restr0.0693894
X-RAY DIFFRACTIONf_plane_restr0.0114966
X-RAY DIFFRACTIONf_dihedral_angle_d21.014841
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.1512745831 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.3922420.3056936X-RAY DIFFRACTION21.81
2.67-2.740.3136780.27391141X-RAY DIFFRACTION27.02
2.74-2.820.3917920.27921491X-RAY DIFFRACTION35.01
2.82-2.910.2982860.28741715X-RAY DIFFRACTION40.04
2.91-3.010.2529990.28161985X-RAY DIFFRACTION46.62
3.01-3.130.30321060.28512325X-RAY DIFFRACTION53.5
3.13-3.280.38041290.2682627X-RAY DIFFRACTION61.56
3.28-3.450.34221510.24562947X-RAY DIFFRACTION68.92
3.45-3.660.34651680.24783433X-RAY DIFFRACTION80.25
3.66-3.950.29752030.22943981X-RAY DIFFRACTION91.88
3.95-4.340.27882510.22024096X-RAY DIFFRACTION97.01
4.34-4.970.27422230.19794152X-RAY DIFFRACTION97.11
4.97-6.260.23151970.21634219X-RAY DIFFRACTION97.76
6.26-45.120.22151800.19544072X-RAY DIFFRACTION94.53

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