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- PDB-4dxu: Crystal Structure of C-lobe of Bovine lactoferrin Complexed with ... -

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Basic information

Entry
Database: PDB / ID: 4dxu
TitleCrystal Structure of C-lobe of Bovine lactoferrin Complexed with aminocaproic acid at 1.46 A Resolution
Components
  • C-TERMINAL PEPTIDE OF Lactotransferrin
  • Lactotransferrin
KeywordsMETAL 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 / antibacterial humoral response / iron ion transport / 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 ...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
6-AMINOHEXANOIC ACID / CARBONATE ION / : / Lactotransferrin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsShukla, P.K. / Gautam, L. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal Structure of C-lobe of Bovine lactoferrin Complexed with aminocaproic acid at 1.46 A Resolution
Authors: Shukla, P.K. / Gautam, L. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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_asym_id / _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_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactotransferrin
B: C-TERMINAL PEPTIDE OF Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,81911
Polymers37,2752
Non-polymers1,5449
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-44 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.655, 49.924, 65.361
Angle α, β, γ (deg.)90.00, 107.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Lactotransferrin / Lactoferrin / Lactoferricin-B / Lfcin-B


Mass: 36622.312 Da / Num. of mol.: 1 / Fragment: C-lobe, UNP residues 361-695 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: P24627, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide C-TERMINAL PEPTIDE OF Lactotransferrin


Mass: 652.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P24627

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Sugars , 2 types, 3 molecules

#3: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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.: 1
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

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Non-polymers , 6 types, 430 molecules

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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-ACA / 6-AMINOHEXANOIC ACID / AMINOCAPROIC ACID


Type: peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Comment: inhibitor*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPROTEINS 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

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.01M ZnSO4, 0.1M MES, 25% PEG, Monomethyl Ether 550 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 9, 2011 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.46→62.4 Å / Num. all: 66980 / Num. obs: 66980 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.044 / Net I/σ(I): 25.5
Reflection shellResolution: 1.46→1.49 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.438 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IB0

3ib0


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
RfactorNum. reflection% reflectionSelection details
Rfree0.18721 3376 5.1 %RANDOM
Rwork0.15824 ---
all0.15971 66980 --
obs0.15971 63217 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.966 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å2-0 Å2-0.51 Å2
2---0.56 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.46→62.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 91 424 3119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.022752
X-RAY DIFFRACTIONr_angle_refined_deg2.6691.9843735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7375339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80325.169118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45615448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5441512
X-RAY DIFFRACTIONr_chiral_restr0.1570.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212053
LS refinement shellResolution: 1.46→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 223 -
Rwork0.244 4473 -
obs--98.39 %

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