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- PDB-1cb6: STRUCTURE OF HUMAN APOLACTOFERRIN AT 2.0 A RESOLUTION. -

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Basic information

Entry
Database: PDB / ID: 1cb6
TitleSTRUCTURE OF HUMAN APOLACTOFERRIN AT 2.0 A RESOLUTION.
ComponentsLactotransferrin
KeywordsIRON TRANSPORT / APOLACTOFERRIN / CONFORMATIONAL CHANGE
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 / negative regulation of osteoclast development / specific granule / 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 / ossification / protein serine/threonine kinase activator activity / secretory granule / innate immune response in mucosa / 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 / antibacterial humoral response / positive regulation of NF-kappaB transcription factor activity / heparin binding / iron ion transport / defense response to Gram-negative bacterium / positive regulation of canonical NF-kappaB signal transduction / killing of cells of another organism / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJameson, G.B. / Anderson, B.F. / Norris, G.E. / Thomas, D.H. / Baker, E.N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of human apolactoferrin at 2.0 A resolution. Refinement and analysis of ligand-induced conformational change.
Authors: Jameson, G.B. / Anderson, B.F. / Norris, G.E. / Thomas, D.H. / 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 A resolution.
Authors: Anderson, B.F. / Baker, H.M. / Norris, G.E. / Rice, D.W. / Baker, E.N.
#3: Journal: Trends Biochem.Sci. / 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-A resolution.
Authors: Anderson, B.F. / Baker, H.M. / Dodson, E.J. / Norris, G.E. / Rumball, S.V. / Waters, J.M. / Baker, E.N.
History
DepositionMar 1, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 12, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 21, 2017Group: Advisory / Database references ...Advisory / Database references / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / pdbx_distant_solvent_atoms / software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _software.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650HELIX DETERMINATION METHOD: AUTHOR-MODIFIED KABSCH & SANDER
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. THE RESIDUES LISTED IN REMARK 500, TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS, ARE IN WELL DEFINED GAMMA-TURNS AT POSITIONALLY HOMOLOGOUS SITES ON BOTH LOBES. THE PEPTIDE BOND IN REMARK 500 AND ITS POSITIONAL HOMOLOG ARE ALSO SUBSTANTIALLY NON-PLANAR IN LACTOFERRIN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3343
Polymers76,2631
Non-polymers712
Water6,431357
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

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Components

#1: Protein Lactotransferrin / Lactoferrin / Growth-inhibiting protein 12 / Talalactoferrin


Mass: 76263.266 Da / Num. of mol.: 1 / Fragment: UNP residues 20-710 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BREAST / Secretion: MILK
References: UniProt: P02788, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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 SEQUENCE USED IN THE X-RAY STRUCTURE FOR RESIDUES 1001-1005 (GRRRS) IS AT VARIANCE WITH THE ...THE SEQUENCE USED IN THE X-RAY STRUCTURE FOR RESIDUES 1001-1005 (GRRRS) IS AT VARIANCE WITH THE MOST RECENT SEQUENCE (SWS P02788, TRFL_H: GRRRRS). IN THIS REGION ELECTRON DENSITY IS POORLY DEFINED AND THE DIFFERENCE IS OF LITTLE STRUCTURAL CONSEQUENCE. THE AMINO ACID SEQUENCE GIVEN IN ENTRY 1LFH REQUIRED CORRECTIONS AT RESIDUE 13 (GLN), 24 (ARG), 28 (LYS), 200 (ARG), 512(GLN)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 53 %
Description: SYNCHROTRON OSCILLATION DATA TO 1.9 A MERGED WITH ENRAF-NONIUS CAD4 DATA TO 2.8 A; DATA TO 2.0 A RETAINED
Crystal growpH: 7.8 / Details: pH 7.8
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein11
20.05 MTris-HCl12
35 %(v/v)MPD12
45 %(v/v)absolute ethanol12

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Type: SRS / Wavelength: 0.87
DetectorDetector: FILM / Details: MIRRORS
RadiationMonochromator: NI MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→17 Å / Num. obs: 53450 / % possible obs: 92 % / Redundancy: 3.3 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 30.3
Reflection shellResolution: 2→2.12 Å / Redundancy: 3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.7 / % possible all: 91
Reflection shell
*PLUS
% possible obs: 91 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ALMNmodel building
SHELXL-97refinement
CCP4(ALMN)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LGF (LACTOFERRIN)

1lgf


Resolution: 2→10 Å / Num. parameters: 22947 / Num. restraintsaints: 22209 / Cross valid method: THROUGHOUT / σ(F): 0
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56. PROLSQ WAS USED FOR INITIAL REFINEMENTS. SHELXL97 WAS USED FOR FINAL REFINEMENTS. THERE IS ...Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56. PROLSQ WAS USED FOR INITIAL REFINEMENTS. SHELXL97 WAS USED FOR FINAL REFINEMENTS. THERE IS POOR DENSITY FOR RESIDUES 1-3. DENSITY FOR RESIDUES 418 - 424 IS POORLY DEFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2146 4 %RANDOM
obs0.201 51304 92 %-
all-53450 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 53.5 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5368 0 2 357 5727
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.003
X-RAY DIFFRACTIONs_angle_d0.01
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.082
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.7
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg19.6

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