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- PDB-1b1x: STRUCTURE OF DIFERRIC MARE LACTOFERRIN AT 2.62A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1b1x
TitleSTRUCTURE OF DIFERRIC MARE LACTOFERRIN AT 2.62A RESOLUTION
ComponentsLACTOFERRIN
KeywordsMETAL 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 / serine-type peptidase activity / regulation of cytokine production / ossification / innate immune response in mucosa / iron ion transport / recycling endosome / antibacterial humoral response / early endosome / negative regulation of apoptotic process / proteolysis / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
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 ...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 speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsSharma, A.K. / Srinivasan, A. / Singh, T.P.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Three-dimensional structure of mare diferric lactoferrin at 2.6 A resolution.
Authors: Sharma, A.K. / Paramasivam, M. / Srinivasan, A. / Yadav, M.P. / Singh, T.P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Purification,Crystallization and Preliminary Crystallographic Analysis of Mare Lactoferrin
Authors: Sharma, A.K. / Karthikeyan, S. / Kaur, P. / Yadav, M.P. / Singh, T.P.
History
DepositionNov 24, 1998Deposition site: BNL / Processing site: RCSB
SupersessionDec 2, 1998ID: 1BGR
Revision 1.0Jun 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)75,6035
Polymers75,3711
Non-polymers2324
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.175, 99.496, 103.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein LACTOFERRIN


Mass: 75371.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Secretion: MILK / References: UniProt: O77811
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growpH: 8.5
Details: 40MG/ML PROTEIN IN 10MM TRIS HCL, PH 8.5, MICRODIALYSED AGA AT 6 DEGREES CELSIUS
Crystal grow
*PLUS
Temperature: 6 ℃ / Method: microdialysis / PH range low: 8.5 / PH range high: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-30 mg/mlprotein11
20.025 MTris-HCl11
310 %(v/v)ethanol12

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1997 / Details: PINHOLE
RadiationMonochromator: GRAPHITE FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.62→15 Å / Num. obs: 25558 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 3.87 % / Biso Wilson estimate: 42.6 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 28.7
Reflection shellResolution: 2.62→2.78 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.29 / Rsym value: 0.25 / % possible all: 72.7
Reflection shell
*PLUS
% possible obs: 80 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN LACTOFERRIN

Resolution: 2.62→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: A POSTERIORI / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2252 9.7 %RANDOM
Rwork0.194 ---
obs-23181 87.8 %-
Displacement parametersBiso mean: 34.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.26 Å
Luzzati d res low-10 Å
Luzzati sigma a0.35 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.62→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5281 0 10 112 5403
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.28
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: 2.62→2.78 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 321 10.2 %
Rwork0.297 2835 -
obs--72.7 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 9.7 % / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.28
LS refinement shell
*PLUS
Rfactor Rfree: 0.351 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.297

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