- PDB-4dxu: Crystal Structure of C-lobe of Bovine lactoferrin Complexed with ... -
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Basic information
Entry
Database: PDB / ID: 4dxu
Title
Crystal Structure of C-lobe of Bovine lactoferrin Complexed with aminocaproic acid at 1.46 A Resolution
Components
C-TERMINAL PEPTIDE OF Lactotransferrin
Lactotransferrin
Keywords
METAL BINDING PROTEIN / C-lobe of lactoferrin / aminocaproic acid / Iron binding protein
Function / homology
Function and homology information
Metal sequestration by antimicrobial proteins / Antimicrobial peptides / 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 ...Metal sequestration by antimicrobial proteins / Antimicrobial peptides / 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 / positive regulation of chondrocyte proliferation / regulation of tumor necrosis factor production / bone morphogenesis / Neutrophil degranulation / cysteine-type endopeptidase inhibitor activity / 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 / recycling endosome / iron ion transport / antibacterial humoral response / early endosome / iron ion binding / serine-type endopeptidase activity / signaling receptor binding / negative regulation of apoptotic process / proteolysis / extracellular space / plasma membrane Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
PROTEINS IN THIS STRUCTURE WERE PREPARED FROM LACTOFERRIN (RESIDUES 1-686) BY PROTEOLYSIS USING ...PROTEINS IN THIS STRUCTURE WERE PREPARED FROM LACTOFERRIN (RESIDUES 1-686) BY PROTEOLYSIS USING SERINE PROTEASE PROTEINASE K. THE ENZYME CUT PROTEIN AT 342, 676, 680 THUS PRODUCING PEPTIDES OF 1-341, 342-676, 677-680, 681-686. CYS 684 FROM THE FRAGMENT 681-686 IS COVALENTLY BONDED TO CYS 405. THIS STRUCTURE CONTAINS PEPTIDE OF 342-676 AND COVALENTLY ATTACHED PEPTIDE 681- 686. (RESIDUE NUMBERING ABOVE FOLLOWS THE COORDINATES. RESIDUES 1-686 CORRESPOND TO RESIDUES 20-705 IN UNIPROTKB/SWISSPROT P24627, TRFL_BOVIN.)
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.62 Å3/Da / Density % sol: 53.02 %
Resolution: 1.46→62.4 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.032 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.059 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.18721
3376
5.1 %
RANDOM
Rwork
0.15824
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all
0.15971
66980
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obs
0.15971
63217
99.46 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 22.966 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.56 Å2
-0 Å2
-0.51 Å2
2-
-
-0.56 Å2
0 Å2
3-
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-0.3 Å2
Refinement step
Cycle: LAST / Resolution: 1.46→62.4 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2604
0
91
424
3119
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.027
0.02
2752
X-RAY DIFFRACTION
r_angle_refined_deg
2.669
1.984
3735
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.737
5
339
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.803
25.169
118
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.456
15
448
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.544
15
12
X-RAY DIFFRACTION
r_chiral_restr
0.157
0.2
424
X-RAY DIFFRACTION
r_gen_planes_refined
0.016
0.021
2053
LS refinement shell
Resolution: 1.46→1.49 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.268
223
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Rwork
0.244
4473
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obs
-
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98.39 %
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