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- PDB-7enu: Crystal structure of iron-saturated C-terminal half of lactoferri... -

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Basic information

Entry
Database: PDB / ID: 7enu
TitleCrystal structure of iron-saturated C-terminal half of lactoferrin produced proteolytically using pepsin at 2.32A resolution
ComponentsLactotransferrin
KeywordsISOMERASE / C-lobe of lactoferrin
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 / specific granule / negative regulation of osteoclast development / 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 / specific granule / negative regulation of osteoclast development / 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
Lactotransferrin / 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
Similarity search - Domain/homology
CARBONATE ION / : / Lactotransferrin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.322 Å
AuthorsSingh, J. / Maurya, A. / Viswanathan, V. / Singh, P.K. / Sharma, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of iron-saturated C-terminal half of lactoferrin produced proteolytically using pepsin at 2.32A resolution
Authors: Singh, J. / Maurya, A. / Viswanathan, V. / Singh, P.K. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionApr 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactotransferrin
B: Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,77512
Polymers76,0242
Non-polymers3,75110
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint27 kcal/mol
Surface area31030 Å2
Unit cell
Length a, b, c (Å)155.670, 82.027, 112.137
Angle α, β, γ (deg.)90.000, 129.624, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lactotransferrin / Lactoferrin


Mass: 38011.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: P24627, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Sugars , 4 types, 6 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 98 molecules

#6: Chemical ChemComp-FE / FE (III) ION


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


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.47 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Magnesium acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2021 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.32→86.38 Å / Num. obs: 47113 / % possible obs: 98.8 % / Redundancy: 3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.036 / Net I/σ(I): 15.1
Reflection shellResolution: 2.32→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3288 / CC1/2: 0.91 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BLF

1blf


Resolution: 2.322→77.748 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.144 / SU ML: 0.219 / Cross valid method: FREE R-VALUE / ESU R: 0.246 / ESU R Free: 0.211
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2487 2275 4.889 %
Rwork0.2029 44254 -
all0.205 --
obs-46529 98.75 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 70 Å2
Baniso -1Baniso -2Baniso -3
1-4.514 Å2-0 Å21.272 Å2
2---7.93 Å20 Å2
3---0.552 Å2
Refinement stepCycle: LAST / Resolution: 2.322→77.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5314 0 244 94 5652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135704
X-RAY DIFFRACTIONr_bond_other_d0.0060.0175222
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.7077760
X-RAY DIFFRACTIONr_angle_other_deg1.2571.63912110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7445694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08323.561264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.79615914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8091526
X-RAY DIFFRACTIONr_chiral_restr0.0660.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026344
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021230
X-RAY DIFFRACTIONr_nbd_refined0.2060.21191
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.24888
X-RAY DIFFRACTIONr_nbtor_refined0.1610.22773
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22674
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2181
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0380.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.210
X-RAY DIFFRACTIONr_nbd_other0.2230.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2430.22
X-RAY DIFFRACTIONr_mcbond_it6.2127.6782782
X-RAY DIFFRACTIONr_mcbond_other6.2067.6772781
X-RAY DIFFRACTIONr_mcangle_it8.76311.5233474
X-RAY DIFFRACTIONr_mcangle_other8.76211.5253475
X-RAY DIFFRACTIONr_scbond_it6.8978.6422922
X-RAY DIFFRACTIONr_scbond_other6.8968.6442923
X-RAY DIFFRACTIONr_scangle_it10.15612.7344286
X-RAY DIFFRACTIONr_scangle_other10.15512.7374287
X-RAY DIFFRACTIONr_lrange_it12.41492.9396163
X-RAY DIFFRACTIONr_lrange_other12.41392.9426164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.322-2.3830.3591540.3593288X-RAY DIFFRACTION99.4798
2.383-2.4480.3741700.3613178X-RAY DIFFRACTION99.554
2.448-2.5190.3731640.3353152X-RAY DIFFRACTION99.8194
2.519-2.5960.3251610.33003X-RAY DIFFRACTION99.4969
2.596-2.6810.3271430.2732927X-RAY DIFFRACTION99.546
2.681-2.7750.3151390.2562818X-RAY DIFFRACTION99.3282
2.775-2.880.3041310.2242732X-RAY DIFFRACTION99.3063
2.88-2.9970.2651260.2172636X-RAY DIFFRACTION98.9964
2.997-3.130.2911320.2222503X-RAY DIFFRACTION98.8743
3.13-3.2830.2711100.2182421X-RAY DIFFRACTION98.7515
3.283-3.460.2971190.2192292X-RAY DIFFRACTION99.0144
3.46-3.670.2611020.2122170X-RAY DIFFRACTION98.3976
3.67-3.9230.226950.1912004X-RAY DIFFRACTION97.5825
3.923-4.2360.2341370.1661840X-RAY DIFFRACTION98.1629
4.236-4.640.2121000.1541743X-RAY DIFFRACTION98.3458
4.64-5.1850.168820.1521585X-RAY DIFFRACTION98.4061
5.185-5.9840.246670.1781382X-RAY DIFFRACTION96.9231
5.984-7.320.231710.1621168X-RAY DIFFRACTION97.1003
7.32-100.195470.139893X-RAY DIFFRACTION95.0455
8-77.7480.219250.219519X-RAY DIFFRACTION94.2808

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