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- PDB-1biy: STRUCTURE OF DIFERRIC BUFFALO LACTOFERRIN -

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Basic information

Entry
Database: PDB / ID: 1biy
TitleSTRUCTURE OF DIFERRIC BUFFALO LACTOFERRIN
ComponentsLACTOFERRIN
KeywordsIRON-BINDING PROTEIN / IRON BINDING PROTEIN / LACTOFERRIN / ANTIBACTERIAL
Function / homology
Function and homology information


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 / regulation of tumor necrosis factor production / bone morphogenesis ...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 / regulation of tumor necrosis factor production / bone morphogenesis / 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 / iron ion transport / recycling endosome / antibacterial humoral response / early endosome / iron ion 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 / 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
CARBONATE ION / : / Lactotransferrin
Similarity search - Component
Biological speciesBubalus bubalis (water buffalo)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.37 Å
AuthorsKarthikeyan, S. / Yadav, S. / Singh, T.P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure of buffalo lactoferrin at 3.3 A resolution at 277 K.
Authors: Karthikeyan, S. / Yadav, S. / Paramasivam, M. / Srinivasan, A. / Singh, T.P.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: Three-Dimensional Structure of Diferric Bovine Lactoferrin at 2.8 A Resolution
Authors: Moore, S.A. / Anderson, B.F. / Groom, C.R. / Haridas, M. / Baker, E.N.
#2: Journal: Arch.Biochem.Biophys. / Year: 1992
Title: Purification, Crystallization, and X-Ray Diffraction Studies of Lactotransferrin from Buffalo Colostrum
Authors: Raman, A. / Bhatia, K.L. / Singh, T.P. / Srinivasan, A. / Betzel, C. / Malik, R.C.
History
DepositionJun 21, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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)76,0945
Polymers75,8621
Non-polymers2324
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.797, 101.436, 76.275
Angle α, β, γ (deg.)90.00, 104.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LACTOFERRIN


Mass: 75862.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bubalus bubalis (water buffalo) / Cellular location: EXTRACELLULAR / Secretion: MILK / References: UniProt: O77698
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.3 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 277 K / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mg/mlprotein11
20.025 MTris-HCl11
319 %(v/v)ethanol12
40.025 MTris-HCl12

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: PINHOLE
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.37→17 Å / Num. obs: 11711 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 3.68 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.0507 / Rsym value: 0.0507 / Net I/σ(I): 34.47
Reflection shellResolution: 3.37→3.58 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 13.35 / Rsym value: 0.135 / % possible all: 97.6
Reflection
*PLUS
Highest resolution: 3.3 Å / % possible obs: 98.5 % / Num. measured all: 42104 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 3.5 Å / % possible obs: 60 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 5.4

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Processing

Software
NameVersionClassification
MARXDSdata collection
MARSCALEdata reduction
AMoREphasing
X-PLOR3.851refinement
MARXDSdata reduction
MARSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN DIFERRIC LACTOFERRIN

Resolution: 3.37→17 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: A POSTERIORI / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1196 10.3 %RANDOM
Rwork0.218 ---
obs0.218 11556 99 %-
Displacement parametersBiso mean: 32.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 17 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 3.37→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5316 0 10 0 5326
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.73
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.37→3.58 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 183 9.9 %
Rwork0.285 1671 -
obs--97.6 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 11711 / Rfactor Rfree: 0.296
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.73

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