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- PDB-3bn6: Crystal Structure of the C2 Domain of Bovine Lactadherin at 1.67 ... -

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Basic information

Entry
Database: PDB / ID: 3bn6
TitleCrystal Structure of the C2 Domain of Bovine Lactadherin at 1.67 Angstrom Resolution
ComponentsLactadherinMFGE8
KeywordsBLOOD CLOTTING / CELL ADHESION / anticoagulation / anti-coagulation / anticoagulant / anti-coagulant / membrane binding / phosphatidyl-serine binding / phosphatidylserine binding / Blood coagulation Factor V C2 homologue / Blood coagulation Factor VIII C2 homologue / milk fat globule / apoptosis / discoidin domain / FA58C / F5_F8_type_C / Alternative splicing / EGF-like domain / Fertilization / Glycoprotein
Function / homology
Function and homology information


acrosomal membrane / single fertilization / angiogenesis / cell adhesion / extracellular region
Similarity search - Function
Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / EGF-like domain / Galactose-binding domain-like / Epidermal growth factor-like domain. / EGF-like domain profile. ...Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / EGF-like domain / Galactose-binding domain-like / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å
AuthorsShao, C. / Novakovic, V.A. / Head, J.F. / Seaton, B.A. / Gilbert, G.E.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of lactadherin C2 domain at 1.7A resolution with mutational and computational analyses of its membrane-binding motif.
Authors: Shao, C. / Novakovic, V.A. / Head, J.F. / Seaton, B.A. / Gilbert, G.E.
History
DepositionDec 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3May 31, 2023Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactadherin


Theoretical massNumber of molelcules
Total (without water)17,9961
Polymers17,9961
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.909, 56.033, 79.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lactadherin / MFGE8 / Milk fat globule-EGF factor 8 / MFG-E8 / MGP57/53 / PAS-6/PAS-7 glycoprotein / MFGM / Sperm surface ...Milk fat globule-EGF factor 8 / MFG-E8 / MGP57/53 / PAS-6/PAS-7 glycoprotein / MFGM / Sperm surface protein SP47 / BP47 / Components 15/16


Mass: 17996.102 Da / Num. of mol.: 1 / Fragment: F5/8 type C 2, C2, residues 270-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: MFGE8 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95114
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 1.98 Å3/Da / Density % sol: 37.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% (w/v) PEG4000, 0.1 M Hepes, pH 7.5, 0.2 M MgCl2, 10% isopropanol, micro-seeding, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 17121 / % possible obs: 98.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.051 / Χ2: 1.29 / Net I/σ(I): 19.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.67-1.7240.33412861.65898.9
1.72-1.774.30.28313091.6199.3
1.77-1.824.20.2112711.54198.8
1.82-1.894.30.1713091.57399.2
1.89-1.964.40.1412761.49898.8
1.96-2.054.50.11113041.38199.2
2.05-2.164.50.0912981.19698.7
2.16-2.34.50.07613151.19299.1
2.3-2.474.60.06613191.0999.6
2.47-2.724.80.05313251.0199.7
2.72-3.124.80.04513461.06299.5
3.12-3.934.70.03813491.14298.8
3.93-504.50.03414141.03496.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.323 / Cor.coef. Fo:Fc: 0.746
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CZT

1czt


Resolution: 1.67→50 Å / FOM work R set: 0.865 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.224 1322 7.7 %
Rwork0.19 --
obs-16784 97.4 %
Solvent computationBsol: 45.56 Å2
Displacement parametersBiso mean: 21.196 Å2
Baniso -1Baniso -2Baniso -3
1--3.637 Å20 Å20 Å2
2--1.301 Å20 Å2
3---2.337 Å2
Refinement stepCycle: LAST / Resolution: 1.67→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 0 233 1507
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1681.5
X-RAY DIFFRACTIONc_scbond_it1.9592
X-RAY DIFFRACTIONc_mcangle_it1.8092
X-RAY DIFFRACTIONc_scangle_it2.8912.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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