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- PDB-1bka: OXALATE-SUBSTITUTED DIFERRIC LACTOFERRIN -

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Basic information

Entry
Database: PDB / ID: 1bka
TitleOXALATE-SUBSTITUTED DIFERRIC LACTOFERRIN
ComponentsLACTOFERRIN
KeywordsIRON BINDING PROTEIN / ANION BINDING
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 / negative regulation of viral process / positive regulation of toll-like receptor 4 signaling pathway / 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 / negative regulation of viral process / positive regulation of toll-like receptor 4 signaling pathway / 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 / positive regulation of protein serine/threonine kinase activity / cysteine-type endopeptidase inhibitor 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 / iron ion transport / 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 / 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 / extracellular space / DNA binding / 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
: / OXALATE ION / Lactotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsBaker, H.M. / Smith, C.A. / Baker, E.N.
Citation
Journal: Biochemistry / Year: 1996
Title: Anion binding by transferrins: importance of second-shell effects revealed by the crystal structure of oxalate-substituted diferric lactoferrin.
Authors: Baker, H.M. / Anderson, B.F. / Brodie, A.M. / Shongwe, M.S. / Smith, C.A. / Baker, E.N.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of Human Diferric Lactoferrin Refined at 2.2 Angstroms Resolution
Authors: Haridas, M. / Anderson, B.F. / Baker, E.N.
#2: Journal: Biochemistry / Year: 1992
Title: Anion Binding by Human Lactoferrin: Results from Crystallographic and Physicochemical Studies
Authors: Shongwe, M.S. / Smith, C.A. / Ainscough, E.W. / Baker, H.M. / Brodie, A.M. / Baker, E.N.
#3: 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.
History
DepositionApr 15, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / 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_database_status.process_site / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)76,5515
Polymers76,2631
Non-polymers2884
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.460, 96.920, 55.850
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 LACTOFERRIN


Mass: 76263.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02788
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 53 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
170 mg/mlprotein11
20.01 Msodium phosphate12
311 %(v/v)methanol12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 15, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 31874 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.115
Reflection
*PLUS
Highest resolution: 2.4 Å
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.54 Å / % possible obs: 83.3 %

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Processing

Software
NameClassification
WEISdata collection
PROLSQrefinement
WEISdata reduction
RefinementResolution: 2.4→8 Å / Num. reflection obs: 31758 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5295 0 14 121 5430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d0.059
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.011
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.248
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

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