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- PDB-4oqo: Crystal structure of the tryptic generated iron-free C-lobe of bo... -

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Basic information

Entry
Database: PDB / ID: 4oqo
TitleCrystal structure of the tryptic generated iron-free C-lobe of bovine Lactoferrin at 2.42 Angstrom resolution
ComponentsLactotransferrinLactoferrin
KeywordsHYDROLASE / c-lobe
Function / homology
Function and homology information


Metal sequestration by antimicrobial proteins / Antimicrobial peptides / negative regulation of cysteine-type endopeptidase activity / 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 lipopolysaccharide-mediated signaling pathway / specific granule / negative regulation of osteoclast development / antifungal humoral response ...Metal sequestration by antimicrobial proteins / Antimicrobial peptides / negative regulation of cysteine-type endopeptidase activity / 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 lipopolysaccharide-mediated signaling pathway / specific granule / negative regulation of osteoclast development / antifungal humoral response / positive regulation of chondrocyte proliferation / regulation of tumor necrosis factor production / bone morphogenesis / Neutrophil degranulation / cysteine-type endopeptidase inhibitor activity / positive regulation of osteoblast proliferation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / innate immune response in mucosa / recycling endosome / antibacterial humoral response / iron ion transport / 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-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin ...Lactotransferrin / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsSingh, A. / Rastogi, N. / Pandey, S. / Bhushan, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: Febs J. / Year: 2014
Title: Structure of the iron-free true C-terminal half of bovine lactoferrin produced by tryptic digestion and its functional significance in the gut.
Authors: Rastogi, N. / Singh, A. / Pandey, S.N. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactotransferrin
B: Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1426
Polymers76,0542
Non-polymers1,0884
Water5,585310
1
A: Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4693
Polymers38,0271
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6733
Polymers38,0271
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.810, 49.440, 97.860
Angle α, β, γ (deg.)90.00, 94.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lactotransferrin / Lactoferrin / Lactoferrin / Lactoferricin-B / Lfcin-B


Mass: 38026.961 Da / Num. of mol.: 2 / Fragment: C-lobe, UNP RESIDUES 361-708 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: P24627, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNATURAL MUTATIONS HAVE OCCURRED AT 584ASN AND 627LYS. AT PRESENT THESE MUTATIONS ARE NOT REPORTED ...NATURAL MUTATIONS HAVE OCCURRED AT 584ASN AND 627LYS. AT PRESENT THESE MUTATIONS ARE NOT REPORTED IN UNIPROT KB.

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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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 8% Tacsimate, 20% PEG 3350, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 27, 2013 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.42→97.58 Å / Num. all: 27691 / Num. obs: 27691 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.097 / Net I/σ(I): 6.8
Reflection shellResolution: 2.42→2.48 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.24 / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TAJ

3taj


Resolution: 2.42→38.67 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.865 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.699 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25988 1386 5 %RANDOM
Rwork0.22288 ---
obs0.22473 26291 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.707 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20.59 Å2
2---0.19 Å2-0 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.42→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5316 0 70 310 5696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195504
X-RAY DIFFRACTIONr_bond_other_d00.025110
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.9657480
X-RAY DIFFRACTIONr_angle_other_deg3.769311764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9075693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.88124.855241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.13315905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3071529
X-RAY DIFFRACTIONr_chiral_restr0.1180.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026275
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021224
X-RAY DIFFRACTIONr_mcbond_it2.4132.7932778
X-RAY DIFFRACTIONr_mcbond_other2.4132.7922777
X-RAY DIFFRACTIONr_mcangle_it3.9574.1823469
X-RAY DIFFRACTIONr_mcangle_other3.9564.1833470
X-RAY DIFFRACTIONr_scbond_it2.5043.152726
X-RAY DIFFRACTIONr_scbond_other2.5043.152726
X-RAY DIFFRACTIONr_scangle_other4.0844.5964012
X-RAY DIFFRACTIONr_long_range_B_refined6.88423.1436614
X-RAY DIFFRACTIONr_long_range_B_other6.88323.1516615
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 102 -
Rwork0.29 1925 -
obs--97.41 %

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