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- PDB-4n6p: Crystal Structure of C-lobe of Bovine lactoferrin complexed with ... -

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Basic information

Entry
Database: PDB / ID: 4n6p
TitleCrystal Structure of C-lobe of Bovine lactoferrin complexed with meclofenamic acid at 1.4 A resolution
Components
  • C-terminal peptide from Lactotransferrin
  • LactotransferrinLactoferrin
KeywordsHYDROLASE / C-LOBE / MECLOFENAMIC ACID
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 ...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 / : / Chem-JMS / Lactotransferrin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGautam, L. / Dube, D. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structre of C-LOBE OF BOVINE LACTOFERRIN COMPLEXED WITH MECLOFENAMIC ACID AT 1.4 A RESOLUTION
Authors: Gautam, L. / Dube, D. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.pdbx_mutation / _entity.src_method
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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

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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 from Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,73712
Polymers37,9102
Non-polymers1,82810
Water5,495305
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-6 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.144, 49.884, 65.210
Angle α, β, γ (deg.)90.00, 106.83, 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 / Lactoferrin / Lactoferricin-B / Lfcin-B


Mass: 37257.055 Da / Num. of mol.: 1 / Fragment: UNP residues 361-695
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Strain: BOVINEBovinae / Production host: Escherichia coli (E. coli)
References: UniProt: P24627, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide C-terminal peptide from Lactotransferrin / Lactoferrin / Lactoferricin-B / Lfcin-B


Mass: 652.759 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Strain: BOVINEBovinae / Production host: Escherichia coli (E. coli) / 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
#8: 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.: 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 , 7 types, 312 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-JMS / 2-[(2,6-dichloro-3-methyl-phenyl)amino]benzoic acid / meclofenamic acid / Meclofenamic acid


Mass: 296.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11Cl2NO2 / Comment: antiinflammatory, inhibitor*YM
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
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: Jul 19, 2013 / 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: 1.4→50 Å / Num. all: 71168 / Num. obs: 71168 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.054 / Net I/σ(I): 42.3
Reflection shellResolution: 1.4→1.42 Å / Mean I/σ(I) obs: 2.6 / Num. unique all: 71168 / Rsym value: 0.561 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RGY

3rgy


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.975 / SU ML: 0.039 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20783 3778 5 %RANDOM
Rwork0.17696 ---
obs0.17852 71168 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.783 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å2-0.92 Å2
2---0.75 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 112 305 3021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0222786
X-RAY DIFFRACTIONr_angle_refined_deg2.7451.9973783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18325.169118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54515448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3571512
X-RAY DIFFRACTIONr_chiral_restr0.1590.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212071
X-RAY DIFFRACTIONr_mcbond_it1.761.51692
X-RAY DIFFRACTIONr_mcangle_it3.05122699
X-RAY DIFFRACTIONr_scbond_it4.28731094
X-RAY DIFFRACTIONr_scangle_it6.9164.51084
LS refinement shellResolution: 1.4→1.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 262 -
Rwork0.283 5057 -
obs--100 %

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