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- PDB-1i6b: STRUCTURE OF EQUINE APOLACTOFERRIN AT 3.2 A RESOLUTION USING CRYS... -

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Basic information

Entry
Database: PDB / ID: 1i6b
TitleSTRUCTURE OF EQUINE APOLACTOFERRIN AT 3.2 A RESOLUTION USING CRYSTALS GROWN AT 303K
ComponentsLACTOTRANSFERRIN
KeywordsMETAL TRANSPORT / Lactoferrin / Equine / Apo / Transferrin / Crystal
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 / bone morphogenesis ...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 / regulation of cytokine production / serine-type peptidase activity / ossification / innate immune response in mucosa / recycling endosome / iron ion transport / antibacterial humoral response / early endosome / negative regulation of apoptotic process / proteolysis / extracellular space / metal ion binding / plasma membrane
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
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKumar, P. / Yadav, S. / Singh, T.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystal structure of equine apolactoferrin at 303 K providing further evidence of closed conformations of N and C lobes.
Authors: Kumar, P. / Khan, J.A. / Yadav, S. / Singh, T.P.
History
DepositionMar 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE RESIDUES IN SEQADV HAD BEEN MODELLED BASED ON THE ELECTRON DENSITY MAPS FOLLOWING THE ...SEQUENCE THE RESIDUES IN SEQADV HAD BEEN MODELLED BASED ON THE ELECTRON DENSITY MAPS FOLLOWING THE REPEATED CYCLES OF REFINEMENT

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LACTOTRANSFERRIN


Theoretical massNumber of molelcules
Total (without water)75,3711
Polymers75,3711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.490, 103.480, 112.270
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 LACTOTRANSFERRIN / LACTOFERRIN


Mass: 75371.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: O77811

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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: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 303 K / Method: microdialysis / pH: 8 / Details: ethanol, pH 8.0, MICRODIALYSIS, temperature 303K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
170 mg/mlprotein11
20.025 MTris-HCl11pH8.0
319 %(v/v)ethanol12

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 16, 2000 / Details: Pinhole
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. all: 50127 / Num. obs: 13457 / % possible obs: 84.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 93.2 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 7
Reflection shellResolution: 3.2→20 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 11 / Num. unique all: 13427 / Rsym value: 0.07 / % possible all: 84.2
Reflection
*PLUS
Num. obs: 15800 / % possible obs: 99.4 % / Num. measured all: 67331 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 94.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MARE DIFFERIC LACTOFERRIN COORDINATES

Resolution: 3.2→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3
RfactorNum. reflection% reflectionSelection details
Rfree0.291 671 5.1 %RANDOM
Rwork0.222 ---
all0.231 50127 --
obs0.222 13184 84.1 %-
Displacement parametersBiso mean: 82.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5281 0 0 0 5281
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_improper_angle_d0.91
X-RAY DIFFRACTIONx_mcbond_it10.851.5
X-RAY DIFFRACTIONx_mcangle_it16.812
X-RAY DIFFRACTIONx_scbond_it2.082
X-RAY DIFFRACTIONx_scangle_it2.682.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 22 3.3 %
Rwork0.367 638 -
obs-60 25.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPO-1.DAT
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 82.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.91
X-RAY DIFFRACTIONx_mcbond_it10.851.5
X-RAY DIFFRACTIONx_scbond_it2.082
X-RAY DIFFRACTIONx_mcangle_it16.812
X-RAY DIFFRACTIONx_scangle_it2.682.5
LS refinement shell
*PLUS
Lowest resolution: 3.4 Å / Rfactor Rfree: 0.4 / % reflection Rfree: 3.3 % / Rfactor Rwork: 0.367

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