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- PDB-1jw1: Crystallization and structure determination of goat lactoferrin a... -

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Basic information

Entry
Database: PDB / ID: 1jw1
TitleCrystallization and structure determination of goat lactoferrin at 4.0 resolution: A new form of packing in lactoferrins with a high solvent content in crystals
ComponentsLACTOFERRIN
KeywordsMETAL BINDING PROTEIN / goat lactoferrin / high solvent content
Function / homology
Function and homology information


: / 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 ...: / 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 / positive regulation of osteoblast proliferation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / monoatomic ion transport / regulation of cytokine production / serine-type peptidase activity / ossification / innate immune response in mucosa / antibacterial humoral response / negative regulation of apoptotic process / extracellular space / metal ion binding
Similarity search - Function
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 ...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
: / Lactotransferrin
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / Resolution: 4 Å
AuthorsKumar, P. / Yadav, S. / Singh, T.P.
CitationJournal: INDIAN J.BIOCHEM.BIOPHYS. / Year: 2002
Title: Crystallization and structure determonation of goat lactoferrin at 4.0A resolution: A new form of packing in lactoferrins with a high solvent content in crystals
Authors: Kumar, P. / Yadav, S. / Singh, T.P.
History
DepositionSep 2, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LACTOFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7323
Polymers75,6201
Non-polymers1122
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.600, 153.800, 155.050
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 LACTOFERRIN


Mass: 75620.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / References: UniProt: Q29477
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe

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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

Crystal growTemperature: 277 K / Method: microdialysis / pH: 8 / Details: ethanol, pH 8.0, MICRODIALYSIS, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 18, 1998
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 15870

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 4→12 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 103755.16 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.328 841 4.9 %RANDOM
Rwork0.228 ---
obs-17327 83 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 1.4948 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2--3.13 Å20 Å2
3----2.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.84 Å0.79 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 4→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5293 0 2 0 5295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2.8
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_improper_angle_d2.49
LS refinement shellResolution: 4→4.24 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 124 4.8 %
Rwork0.226 2460 -
obs--75.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3ion.paramion.top

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