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- PDB-2bjj: Structure of recombinant human lactoferrin produced in the milk o... -

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Basic information

Entry
Database: PDB / ID: 2bjj
TitleStructure of recombinant human lactoferrin produced in the milk of transgenic cows
ComponentsLACTOTRANSFERRIN
KeywordsMETAL BINDING PROTEIN / METAL-BINDING PROTEIN / LACTOFERRIN / TRANSGENIC COWS / IRON-BINDING / ANTIBIOTIC / GLYCOPROTEIN / POLYMORPHISM
Function / homology
Function and homology information


negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / negative regulation of viral process / 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 ...negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / negative regulation of viral process / 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 / negative regulation of ATP-dependent activity / regulation of tumor necrosis factor production / bone morphogenesis / Antimicrobial peptides / cysteine-type endopeptidase inhibitor activity / negative regulation of viral genome replication / positive regulation of osteoblast proliferation / humoral immune response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / regulation of cytokine production / protein serine/threonine kinase activator activity / ossification / innate immune response in mucosa / secretory granule / lipopolysaccharide binding / positive regulation of protein serine/threonine kinase activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / positive regulation of NF-kappaB transcription factor activity / heparin binding / iron ion transport / antibacterial humoral response / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / killing of cells of another organism / early endosome / iron ion binding / Amyloid fiber formation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein-containing complex / proteolysis / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm
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 ...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 / 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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsThomassen, E.A.J. / Van Veen, H.A. / Van Berkel, P.H.C. / Nuijens, J.H. / Abrahams, J.P.
Citation
Journal: Transgenic Res. / Year: 2005
Title: The Protein Structure of Recombinant Human Lactoferrin Produced in the Milk of Transgenic Cows Closely Matches the Structure of Human Milk-Derived Lactoferrin
Authors: Thomassen, E.A.J. / Van Veen, H.A. / Van Berkel, P.H.C. / Nuijens, J.H. / Abrahams, J.P.
#1: Journal: Nat.Biotechnol. / Year: 2002
Title: Large Scale Production of Recombinant Human Lactoferrin in the Milk of Transgenic Cows
Authors: Van Berkel, P.H.C. / Welling, M.M. / Geerts, M. / Van Veen, H.A. / Ravensbergen, B. / Salaheddine, M. / Pauwels, E.K.J. / Pieper, F. / Nuijens, J.N. / Nibbering, P.H.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of Human Diferric Lactoferrin Refined at 2.2 Angstrom Resolution
Authors: Haridas, M. / Anderson, B.F. / Baker, E.N.
History
DepositionFeb 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: LACTOTRANSFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1097
Polymers76,4341
Non-polymers6746
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.941, 97.379, 156.297
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 / LACTOFERRIN / RECOMBINANT HUMAN LACTOFERRIN


Mass: 76434.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: EXPRESSED IN TRANSGENIC COW / Production host: BOS TAURUS (cattle) / References: UniProt: P02788
#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: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.62 %
Crystal growpH: 8.5 / Details: 5 MM SODIUM PHOSPHATE PH 8.5, 10% (V/V) ETHANOL

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 29, 2003 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→81.65 Å / Num. obs: 33492 / % possible obs: 96.2 % / Observed criterion σ(I): 3.5 / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LFG

1lfg


Resolution: 2.4→19.63 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.083 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1640 5.1 %RANDOM
Rwork0.181 ---
obs0.184 30833 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.28 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å20 Å2
2---0.5 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5357 0 38 54 5449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225533
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9637496
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1015694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4623.672256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.71215921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.941546
X-RAY DIFFRACTIONr_chiral_restr0.1020.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024250
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.22202
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23725
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.220
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9631.53535
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66625523
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.11532248
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.484.51972
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 126 -
Rwork0.246 2265 -
obs--97.39 %

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