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- PDB-2pqs: Crystal Structure of the Bovine Lactadherin C2 Domain -

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Basic information

Entry
Database: PDB / ID: 2pqs
TitleCrystal Structure of the Bovine Lactadherin C2 Domain
ComponentsLactadherin
KeywordsCELL ADHESION / C2 domain / lactadherin / membrane binding
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. ...: / 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 1. / EGF-like domain signature 2. / EGF-like domain / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHuang, M. / Furie, B.C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of the bovine lactadherin C2 domain, a membrane binding motif, shows similarity to the C2 domains of factor V and factor VIII.
Authors: Lin, L. / Huai, Q. / Huang, M. / Furie, B. / Furie, B.C.
History
DepositionMay 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactadherin
B: Lactadherin
C: Lactadherin
D: Lactadherin


Theoretical massNumber of molelcules
Total (without water)72,3814
Polymers72,3814
Non-polymers00
Water2,144119
1
A: Lactadherin


Theoretical massNumber of molelcules
Total (without water)18,0951
Polymers18,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lactadherin


Theoretical massNumber of molelcules
Total (without water)18,0951
Polymers18,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lactadherin


Theoretical massNumber of molelcules
Total (without water)18,0951
Polymers18,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lactadherin


Theoretical massNumber of molelcules
Total (without water)18,0951
Polymers18,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.123, 107.788, 82.754
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Lactadherin / 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: 18095.232 Da / Num. of mol.: 4 / Fragment: C2 domain (Residues 270-427)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: MFGE8 / Plasmid: pPICz / Production host: Pichia pastoris (fungus) / References: UniProt: Q95114
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 7.5
Details: 15% PEG4K, 20% glycerol, 50 mM HEPES, pH 7.5, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorDetector: IMAGE PLATE
RadiationMonochromator: Si(111) channel-cut crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 19426 / Num. obs: 19057 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.26 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1171545.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1169 3.1 %RANDOM
Rwork0.235 ---
obs0.235 38256 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.6315 Å2 / ksol: 0.339252 e/Å3
Displacement parametersBiso mean: 44.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.73 Å20 Å20 Å2
2---8.05 Å20 Å2
3---14.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5100 0 0 119 5219
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.791.5
X-RAY DIFFRACTIONc_mcangle_it4.152
X-RAY DIFFRACTIONc_scbond_it4.542
X-RAY DIFFRACTIONc_scangle_it5.842.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 205 3.3 %
Rwork0.323 6091 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2lac2.par
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param

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