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- PDB-1l5t: Crystal Structure of a Domain-Opened Mutant (R121D) of the Human ... -

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Basic information

Entry
Database: PDB / ID: 1l5t
TitleCrystal Structure of a Domain-Opened Mutant (R121D) of the Human Lactoferrin N-lobe Refined From a Merohedrally-Twinned Crystal Form.
Componentslactoferrin
KeywordsMETAL TRANSPORT / IRON TRANSPORT / GLYCOPROTEIN / LACTOFERRIN / N-LOBE / IRON-RELEASE / TWINNING
Function / homology
Function and homology information


membrane destabilizing activity / host-mediated suppression of viral proces / Mtb iron assimilation by chelation / phagocytic vesicle lumen / Metal sequestration by antimicrobial proteins / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of viral process / 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 ...membrane destabilizing activity / host-mediated suppression of viral proces / Mtb iron assimilation by chelation / phagocytic vesicle lumen / Metal sequestration by antimicrobial proteins / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of viral process / 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 osteoclast development / antifungal humoral response / specific granule / negative regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of chondrocyte proliferation / negative regulation of ATP-dependent activity / regulation of tumor necrosis factor production / bone morphogenesis / Antimicrobial peptides / 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 protein serine/threonine kinase activity / cysteine-type endopeptidase inhibitor activity / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / secretory granule / protein serine/threonine kinase activator activity / innate immune response in mucosa / lipopolysaccharide binding / iron ion transport / positive regulation of NF-kappaB transcription factor activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / tertiary granule lumen / heparin binding / defense response to Gram-negative bacterium / killing of cells of another organism / early endosome / positive regulation of canonical NF-kappaB signal transduction / iron ion binding / Amyloid fiber formation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein-containing complex / proteolysis / extracellular space / DNA binding / 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 / Transferrin-like domain / 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 / Transferrin-like domain / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJameson, G.B. / Anderson, B.F. / Breyer, W.A. / Tweedie, J.W. / Baker, E.N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of a domain-opened mutant (R121D) of the human lactoferrin N-lobe refined from a merohedrally twinned crystal form.
Authors: Jameson, G.B. / Anderson, B.F. / Breyer, W.A. / Day, C.L. / Tweedie, J.W. / Baker, E.N.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: On the Molecular-Replacement Problem in the Presence of Merohedral Twinning: Structure of the N-Terminal Half-Molecule of Human Lactoferrin
Authors: Breyer, W.A. / Kingston, R.L. / Anderson, B.F. / Baker, E.N.
History
DepositionMar 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lactoferrin
B: lactoferrin


Theoretical massNumber of molelcules
Total (without water)73,8442
Polymers73,8442
Non-polymers00
Water2,288127
1
A: lactoferrin


Theoretical massNumber of molelcules
Total (without water)36,9221
Polymers36,9221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: lactoferrin


Theoretical massNumber of molelcules
Total (without water)36,9221
Polymers36,9221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.300, 151.300, 48.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein lactoferrin / LACTOTRANSFERRIN


Mass: 36921.875 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-352 / Mutation: R121D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pnut / Cell line (production host): BHK / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02788, EC: 1.16.1.2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.35 Å3/Da / Density % sol: 71.7 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 8
Details: concentrated solution of the protein (50-80 mg mL-1), 0.01 M Tris-HCl, pH 8.0, 12% (v/v) isopropanol, MICRODIALYSIS, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.05 MTris-HCl1droppH8.0
20.1 M1dropNaCl
30.01 Mferric nitrilotriacetate1drop
450-80 mg/mlprotein1drop
50.01 MTris-HCl1reservoirpH8.0
612 %(v/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1994 / Details: graphite monochromator
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 23431 / % possible obs: 96 % / Observed criterion σ(F): 4 / Redundancy: 2.8 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 6.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.418 / % possible all: 93
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 23882 / % possible obs: 96 %
Reflection shell
*PLUS
Highest resolution: 3 Å / % possible obs: 93 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATAdata reduction
X-PLORmodel building
BRUTEmodel building
SHELXL-97refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
BRUTEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1lct

1lct


Resolution: 3→10 Å / Num. parameters: 19883 / Num. restraintsaints: 27798
Isotropic thermal model: INDIVIDUAL, WITH TIGHT ADJACENCY AND NCS RESTRAINTS, AND IDENTITY CONSTRAINTS ON NEARLY CHEMICALLY EQUIVALENT REDIDUES (E.G. OE1 AND OE2 OF GLU)
Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: WEIGHTED CONJUGATE-GRADIENT REFINEMENT ON F-SQUARED; HEMIHEDRAL TWINNING TO GIVE PSEUDO-HEXAGONAL (6/M) DIFFRACTION SYMMETRY; TWIN RATIO=0.44035:0.54965. WITH REGARDS TO THE TORSION ANGLES ...Details: WEIGHTED CONJUGATE-GRADIENT REFINEMENT ON F-SQUARED; HEMIHEDRAL TWINNING TO GIVE PSEUDO-HEXAGONAL (6/M) DIFFRACTION SYMMETRY; TWIN RATIO=0.44035:0.54965. WITH REGARDS TO THE TORSION ANGLES OF LEU 299, THE RESIDUE IS PART OF A CONSERVED GAMMA TURN.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 795 -RANDOM, PLUS TWIN-RELATED MATES
Rwork0.139 ---
all0.1413 23431 --
obs-21955 93.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, 1975 K(SOLV)=0.551302, B(SOLV)=2.7660
Bsol: 2.766 Å2 / ksol: 0.551302 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5241
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5114 0 0 127 5241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.017
X-RAY DIFFRACTIONs_similar_dist0.012
X-RAY DIFFRACTIONs_from_restr_planes0.177
X-RAY DIFFRACTIONs_zero_chiral_vol0.023
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.026
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 3→3.11 Å
RfactorNum. reflection% reflection
Rfree0.287 74 -
Rwork0.239 --
obs-2267 93 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. reflection obs: 22636
Solvent computation
*PLUS
Displacement parameters
*PLUS

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