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- PDB-1lfh: MOLECULAR REPLACEMENT SOLUTION OF THE STRUCTURE OF APOLACTOFERRIN... -

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Basic information

Entry
Database: PDB / ID: 1lfh
TitleMOLECULAR REPLACEMENT SOLUTION OF THE STRUCTURE OF APOLACTOFERRIN, A PROTEIN DISPLAYING LARGE-SCALE CONFORMATIONAL CHANGE
ComponentsLACTOFERRIN
KeywordsIRON TRANSPORT
Function / homology
Function and homology information


host-mediated suppression of viral proces / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / Metal sequestration by antimicrobial proteins / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of viral process / 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 ...host-mediated suppression of viral proces / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / Metal sequestration by antimicrobial proteins / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of viral process / 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 / negative regulation of ATP-dependent activity / regulation of tumor necrosis factor production / bone morphogenesis / Antimicrobial peptides / negative regulation of viral genome replication / positive regulation of osteoblast proliferation / humoral immune response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cysteine-type endopeptidase inhibitor activity / positive regulation of protein serine/threonine kinase activity / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / secretory granule / protein serine/threonine kinase activator activity / innate immune response in mucosa / lipopolysaccharide binding / positive regulation of NF-kappaB transcription factor activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / tertiary granule lumen / heparin binding / iron ion transport / defense response to Gram-negative bacterium / killing of cells of another organism / early endosome / positive regulation of canonical NF-kappaB signal transduction / 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 / Transferrin-like domain / 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 / Transferrin-like domain / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsAnderson, B.F. / Baker, E.N. / Norris, G.E.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Molecular replacement solution of the structure of apolactoferrin, a protein displaying large-scale conformational change.
Authors: Norris, G.E. / Anderson, B.F. / Baker, E.N.
#1: Journal: Nature / Year: 1990
Title: Apolactoferrin Structure Demonstrates Ligand-Induced Conformational Change in Transferrins
Authors: Anderson, B.F. / Baker, H.M. / Norris, G.E. / Rumball, S.V. / Baker, E.N.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Structure of Human Lactoferrin: Crystallographic Structure Analysis and Refinement at 2.8 Angstroms Resolution
Authors: Anderson, B.F. / Baker, H.M. / Norris, G.E. / Rice, D.W. / Baker, E.N.
#3: Journal: Trends Biochem.Sci.(Pers. Ed.) / Year: 1987
Title: Transferrins: Insights Into Structure and Function from Studies on Lactoferrin
Authors: Baker, E.N. / Rumball, S.V. / Anderson, B.F.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Structure of Human Lactoferrin at 3.2 Angstroms Resolution
Authors: Anderson, B.F. / Baker, H.M. / Dodson, E.J. / Norris, G.E. / Rumball, S.V. / Waters, J.M. / Baker, E.N.
History
DepositionSep 4, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 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 / 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_entry_details.has_protein_modification / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS ...SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS *N2A* AND *N2B* REPRESENT ONE BIFURCATED SHEET AND STRAND FOUR OF SHEET BN1 IS ALSO PART OF THIS SHEET. SHEETS *C2A* AND *C2B* REPRESENT ONE BIFURCATED SHEET AND STRAND FOUR OF SHEET BC1 IS ALSO PART OF THIS SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LACTOFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2582
Polymers76,2221
Non-polymers351
Water6,720373
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.090, 94.580, 55.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 71 / 2: CIS PROLINE - PRO 142 / 3: CIS PROLINE - PRO 628

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Components

#1: Protein LACTOFERRIN


Mass: 76222.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02788
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS A TWO FOLD INTERNAL SEQUENCE HOMOLOGY (~40% IDENTITY).
Has protein modificationY
Sequence detailsTHE AMINO ACID SEQUENCE GIVEN IN ANDERSON ET AL. (1989). WAS FOLLOWED IN BUILDING THE MODEL. THIS ...THE AMINO ACID SEQUENCE GIVEN IN ANDERSON ET AL. (1989). WAS FOLLOWED IN BUILDING THE MODEL. THIS PAPER REPORTS CORRECTIONS TO THE AMINO ACID SEQUENCE REPORTED IN THE SEQUENCE DATABASES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.8 / Method: microdialysis
Details: taken from Baker, E.N. et al (1977). J. Mol. Biol., 111, 207-210.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-5 %protein11
20.01 Mphosphate12
310 %(v/v)ethanol12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. obs: 17783 / Num. measured all: 19413 / Rmerge(I) obs: 0.09

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.213 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5342 0 1 373 5716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 10 Å / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS

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