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- PDB-1fck: STRUCTURE OF DICERIC HUMAN LACTOFERRIN -

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Basic information

Entry
Database: PDB / ID: 1fck
TitleSTRUCTURE OF DICERIC HUMAN LACTOFERRIN
ComponentsLACTOFERRIN
KeywordsMETAL TRANSPORT / transferrin / metal-binding / cerium / lanthanide
Function / homology
Function and homology information


negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / negative regulation of viral process / 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 ...negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / negative regulation of viral process / 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 / negative regulation of ATP-dependent activity / positive regulation of chondrocyte proliferation / regulation of tumor necrosis factor production / bone morphogenesis / Antimicrobial peptides / cysteine-type endopeptidase inhibitor activity / negative regulation of viral genome replication / positive regulation of osteoblast proliferation / humoral immune response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / regulation of cytokine production / protein serine/threonine kinase activator activity / ossification / innate immune response in mucosa / secretory granule / lipopolysaccharide binding / positive regulation of protein serine/threonine kinase activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / heparin binding / positive regulation of NF-kappaB transcription factor activity / antibacterial humoral response / iron ion transport / positive regulation of canonical NF-kappaB signal transduction / killing of cells of another organism / defense response to Gram-negative bacterium / early endosome / iron ion binding / Amyloid fiber formation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein-containing complex / proteolysis / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm
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
CERIUM (III) ION / CARBONATE ION / Lactotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsBaker, H.M. / Baker, C.J. / Smith, C.A. / Baker, E.N.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2000
Title: Metal substitution in transferrins: specific binding of cerium(IV) revealed by the crystal structure of cerium-substituted human lactoferrin.
Authors: Baker, H.M. / Baker, C.J. / Smith, C.A. / Baker, E.N.
History
DepositionJul 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LACTOFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8075
Polymers76,4061
Non-polymers4004
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.9, 97.1, 56.0
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein LACTOFERRIN /


Mass: 76406.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02788
#2: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-CE / CERIUM (III) ION / Cerium


Mass: 140.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ce
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal grow
*PLUS
pH: 8 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160 mg/mlprotein11
20.01 MTris-HCl12
310 %(v/v)ethanol12

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Feb 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 35878 / % possible obs: 81.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.8
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.341 / % possible all: 64.3
Reflection
*PLUS
Num. obs: 35878
Reflection shell
*PLUS
Lowest resolution: 2.35 Å / % possible obs: 64.3 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
RefinementHighest resolution: 2.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 3585 10 %Random
Rwork0.2025 ---
all-35856 --
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5324 0 10 152 5486
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0059
X-RAY DIFFRACTIONc_angle_deg1.307
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS

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