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- PDB-7fdw: Crystal structure of pepsin cleaved lactoferrin C-lobe at 2.28 A ... -

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Basic information

Entry
Database: PDB / ID: 7fdw
TitleCrystal structure of pepsin cleaved lactoferrin C-lobe at 2.28 A resolution
ComponentsLactotransferrinLactoferrin
KeywordsHYDROLASE / 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 / antibacterial humoral response / iron ion transport / early endosome / iron ion binding / signaling receptor 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-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: 2.277 Å
AuthorsSingh, P.K. / Singh, J. / Maurya, A. / Sharma, P. / Sharma, S. / Singh, T.P.
CitationJournal: Protein J. / Year: 2021
Title: A Peptide Bond from the Inter-lobe Segment in the Bilobal Lactoferrin Acts as a Preferred Site for Cleavage for Serine Proteases to Generate the Perfect C-lobe: Structure of the Pepsin ...Title: A Peptide Bond from the Inter-lobe Segment in the Bilobal Lactoferrin Acts as a Preferred Site for Cleavage for Serine Proteases to Generate the Perfect C-lobe: Structure of the Pepsin Hydrolyzed Lactoferrin C-lobe at 2.28 angstrom Resolution.
Authors: Singh, J. / Maurya, A. / Singh, P.K. / Viswanathan, V. / Ahmad, M.I. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionJul 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactotransferrin
B: Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,45811
Polymers76,0242
Non-polymers2,4349
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint15 kcal/mol
Surface area29640 Å2
Unit cell
Length a, b, c (Å)153.781, 81.703, 111.694
Angle α, β, γ (deg.)90.000, 129.857, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 342 - 689 / Label seq-ID: 1 - 348

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lactotransferrin / Lactoferrin / 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 , 2 types, 5 molecules

#2: 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.: 3
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
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 260 molecules

#3: Chemical ChemComp-FE / FE (III) ION / Iron


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


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.55 Å3/Da / Density % sol: 65 %
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: BM30A / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.277→76.7 Å / Num. obs: 48821 / % possible obs: 98.8 % / Redundancy: 3 % / CC1/2: 0.97 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.6
Reflection shellResolution: 2.277→2.31 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3392 / CC1/2: 0.94 / % possible all: 99.8

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Processing

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

1blf


Resolution: 2.277→76.7 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: FREE R-VALUE / ESU R: 0.247 / ESU R Free: 0.203
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2469 2465 5.11 %
Rwork0.2126 45776 -
all0.214 --
obs-48241 98.814 %
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
1-0.788 Å20 Å20.92 Å2
2---8.288 Å2-0 Å2
3---2.492 Å2
Refinement stepCycle: LAST / Resolution: 2.277→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5314 0 155 256 5725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135596
X-RAY DIFFRACTIONr_bond_other_d0.0360.0175155
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.6837614
X-RAY DIFFRACTIONr_angle_other_deg2.5181.61911938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.465694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29523.561264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.01315914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2381526
X-RAY DIFFRACTIONr_chiral_restr0.0660.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026313
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021224
X-RAY DIFFRACTIONr_nbd_refined0.2020.21237
X-RAY DIFFRACTIONr_symmetry_nbd_other0.230.24945
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22733
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2310.29
X-RAY DIFFRACTIONr_metal_ion_refined0.0120.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.216
X-RAY DIFFRACTIONr_nbd_other0.2710.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.25
X-RAY DIFFRACTIONr_mcbond_it7.1767.7932782
X-RAY DIFFRACTIONr_mcbond_other7.1697.7912781
X-RAY DIFFRACTIONr_mcangle_it9.99511.6893474
X-RAY DIFFRACTIONr_mcangle_other9.99311.693475
X-RAY DIFFRACTIONr_scbond_it7.1148.5062814
X-RAY DIFFRACTIONr_scbond_other7.1168.5112812
X-RAY DIFFRACTIONr_scangle_it10.37612.5034140
X-RAY DIFFRACTIONr_scangle_other10.37812.5074138
X-RAY DIFFRACTIONr_lrange_it15.244149.42223865
X-RAY DIFFRACTIONr_lrange_other15.265149.5523728
X-RAY DIFFRACTIONr_ncsr_local_group_10.0820.0511009
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.08170.05009
12BX-RAY DIFFRACTIONLocal ncs0.08170.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.277-2.3360.3421910.3353392X-RAY DIFFRACTION99.6939
2.336-2.40.341770.343306X-RAY DIFFRACTION99.7137
2.4-2.4690.3361530.313247X-RAY DIFFRACTION99.9118
2.469-2.5450.3061660.2813123X-RAY DIFFRACTION99.6969
2.545-2.6280.2981510.2473041X-RAY DIFFRACTION99.0997
2.628-2.7210.2761550.2392966X-RAY DIFFRACTION99.5852
2.721-2.8230.2921580.2432785X-RAY DIFFRACTION99.325
2.823-2.9380.2771590.2322640X-RAY DIFFRACTION97.3227
2.938-3.0690.31380.2262603X-RAY DIFFRACTION98.846
3.069-3.2180.2861290.2452500X-RAY DIFFRACTION99.3575
3.218-3.3920.3011280.2312391X-RAY DIFFRACTION99.4473
3.392-3.5980.254960.2182249X-RAY DIFFRACTION99.1543
3.598-3.8460.2731270.2072089X-RAY DIFFRACTION98.4889
3.846-4.1530.2061060.1761964X-RAY DIFFRACTION98.5714
4.153-4.5480.2191220.1611769X-RAY DIFFRACTION97.9285
4.548-5.0830.194830.1641615X-RAY DIFFRACTION97.4742
5.083-5.8660.239710.191407X-RAY DIFFRACTION95.232
5.866-7.1760.246770.1891195X-RAY DIFFRACTION96.5831
7.176-100.151490.151952X-RAY DIFFRACTION97.5633
8-100.215290.215542X-RAY DIFFRACTION95.0083

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