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- PDB-1f9b: MELANIN PROTEIN INTERACTION: X-RAY STRUCTURE OF THE COMPLEX OF MA... -

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Basic information

Entry
Database: PDB / ID: 1f9b
TitleMELANIN PROTEIN INTERACTION: X-RAY STRUCTURE OF THE COMPLEX OF MARE LACTOFERRIN WITH MELANIN MONOMERS
ComponentsLACTOTRANSFERRIN
KeywordsMETAL TRANSPORT / Lactoferrin / IDQ molecule / complex / melanin / IRON TRANSPORT / METAL-BINDING
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 lipopolysaccharide-mediated signaling pathway / negative regulation of osteoclast development / specific granule / antifungal humoral response / 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 lipopolysaccharide-mediated signaling pathway / negative regulation of osteoclast development / specific granule / antifungal humoral response / 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 / serine-type peptidase activity / ossification / innate immune response in mucosa / recycling endosome / antibacterial humoral response / iron ion transport / 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-like domain / Transferrin / 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-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
3H-INDOLE-5,6-DIOL / BICARBONATE ION / : / Lactotransferrin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsKumar, S. / Singh, T.P. / Sharma, A.K. / Singh, N. / Raman, G.
Citation
Journal: Proteins / Year: 2001
Title: Lactoferrin-melanin interaction and its possible implications in melanin polymerization: crystal structure of the complex formed between mare lactoferrin and melanin monomers at 2.7-A resolution.
Authors: Sharma, A.K. / Kumar, S. / Sharma, V. / Nagpal, A. / Singh, N. / Tamboli, I. / Mani, I. / Raman, G. / Singh, T.P.
#1: Journal: Indian J.Physics / Year: 2000
Title: Metal Substitution in Lactoferrins: the Crystal Structure of Manganese Lactoferrin at 3.4 A
History
DepositionJul 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Oct 30, 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 / 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.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

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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)76,6187
Polymers76,0861
Non-polymers5326
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.037, 99.815, 103.425
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


Mass: 76086.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Secretion: MILK-COLUSTRUM / 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-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-3ID / 3H-INDOLE-5,6-DIOL


Mass: 149.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 5
Details: 20mM Tris-Hcl, pH 5.0 concentration 50 mg/ml 10% ethanol soaked for 12hours in buffer containing DOPA, MICRODIALYSIS, temperature 4K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMTris-HCl11
250 mg/mlprotein11
310 %ethanol12

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 7, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→15 Å / Num. all: 18557 / Num. obs: 18557 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 3.6
Reflection shellResolution: 2.7→15 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.124 / Num. unique all: 18557 / % possible all: 91
Reflection
*PLUS
% possible obs: 91 % / Num. measured all: 100340 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
Lowest resolution: 2.9 Å / % possible obs: 63 % / Rmerge(I) obs: 0.142

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Processing

Software
NameClassification
DENZOdata reduction
AUTOMARdata reduction
AMoREphasing
X-PLORrefinement
RefinementResolution: 2.7→15 Å / σ(F): 0 / σ(I): 0
Stereochemistry target values: 84% most allowed region and 2 residues are in disallowed region 299, 640 due to gama turn.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 463 -2.5% of the observed reflection
Rwork0.215 ---
all0.287 18557 --
obs0.215 18557 91 %-
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5281 0 32 73 5386
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONBond angles2
X-RAY DIFFRACTIONBond lengths0.014
X-RAY DIFFRACTIONDihedral angles23.9
X-RAY DIFFRACTIONImproper angles1.7
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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