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- PDB-3tod: Crystal Structure of C-lobe of Bovine lactoferrin Complexed with ... -

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Basic information

Entry
Database: PDB / ID: 3tod
TitleCrystal Structure of C-lobe of Bovine lactoferrin Complexed with 1-Butyl-1H-Pyrazole-5-carboxylic acid at 1.38 A Resolution
Components
  • Lactotransferrin
  • peptide, LEACAF from Lactotransferrin
KeywordsHYDROLASE / C-LOBE / Metal binding protein / 1- butyl1-h-pyrazol-5-carboxylic 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 / 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 ...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 / ETHANOL / : / 1-butyl-1H-pyrazole-5-carboxylic acid / Lactotransferrin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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 1-Butyl-1H-Pyrazole-5-carboxylic acid at 1.38 A Resolution
Authors: Shukla, P.K. / Gautam, L. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionSep 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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: peptide, LEACAF from Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,33615
Polymers37,2752
Non-polymers2,06013
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-35 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.415, 49.977, 65.289
Angle α, β, γ (deg.)90.00, 107.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide / Sugars , 3 types, 5 molecules AB

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


Mass: 36622.312 Da / Num. of mol.: 1 / Fragment: C-lobe, UNP residues 361-705 / 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 peptide, LEACAF from Lactotransferrin


Mass: 652.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P24627
#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.: 3
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

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Non-polymers , 8 types, 559 molecules

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


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


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


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


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#10: Chemical ChemComp-XXB / 1-butyl-1H-pyrazole-5-carboxylic acid


Mass: 168.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHERE ARE CONFLICTS BETWEEN SEQRES(LYS A 565, GLU A 608) AND SEQUENCE DATABASE (ASN, LYS). AUTHORS ...THERE ARE CONFLICTS BETWEEN SEQRES(LYS A 565, GLU A 608) AND SEQUENCE DATABASE (ASN, LYS). AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND IS THE TRUE IDENTITY OF THESE RESIDUES AND IS NATURAL MUTANT.

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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: 2.61 Å3/Da / Density % sol: 52.88 %
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 16, 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: 1.38→62.39 Å / Num. all: 79168 / Num. obs: 72933 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.0802 / Net I/σ(I): 18.2
Reflection shellResolution: 1.38→1.43 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.389 / % possible all: 91.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IB0

3ib0


Resolution: 1.38→62.39 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23621 3867 5 %RANDOM
Rwork0.19969 ---
all0.20156 79168 --
obs0.20156 72933 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.178 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.65 Å2
2---0.74 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.38→62.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 126 549 3280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0222786
X-RAY DIFFRACTIONr_angle_refined_deg2.4221.9963778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5995339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74625.169118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16115448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9331512
X-RAY DIFFRACTIONr_chiral_restr0.1590.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212069
X-RAY DIFFRACTIONr_mcbond_it1.6951.51695
X-RAY DIFFRACTIONr_mcangle_it2.6922703
X-RAY DIFFRACTIONr_scbond_it3.64431091
X-RAY DIFFRACTIONr_scangle_it5.6724.51075
LS refinement shellResolution: 1.38→1.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 266 -
Rwork0.458 4976 -
obs--89.99 %

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