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- PDB-6los: Crystal structure of mouse PEDF in complex with heterotrimeric co... -

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Basic information

Entry
Database: PDB / ID: 6los
TitleCrystal structure of mouse PEDF in complex with heterotrimeric collagen model peptide.
Components
  • (Collagen model peptide, type I, alpha ...) x 3
  • Pigment epithelium-derived factor
KeywordsSIGNALING PROTEIN / Serpins / Collagen binding protein / Anti-angiogenesis
Function / homology
Function and homology information


: / cellular response to cobalt ion / response to peptide / : / negative regulation of epithelial cell proliferation involved in prostate gland development / short-term memory / negative regulation of endopeptidase activity / axon hillock / response to arsenic-containing substance / response to acidic pH ...: / cellular response to cobalt ion / response to peptide / : / negative regulation of epithelial cell proliferation involved in prostate gland development / short-term memory / negative regulation of endopeptidase activity / axon hillock / response to arsenic-containing substance / response to acidic pH / ovulation cycle / negative regulation of endothelial cell migration / positive regulation of neurogenesis / basement membrane / cellular response to retinoic acid / negative regulation of angiogenesis / cellular response to dexamethasone stimulus / kidney development / cellular response to glucose stimulus / serine-type endopeptidase inhibitor activity / response to organic cyclic compound / positive regulation of neuron projection development / negative regulation of inflammatory response / melanosome / retina development in camera-type eye / axon / negative regulation of gene expression / neuronal cell body / perinuclear region of cytoplasm / extracellular space / extracellular region
Similarity search - Function
Pigment epithelium derived factor, serpin domain / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
Pigment epithelium-derived factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.476 Å
AuthorsKawahara, K. / Maruno, T. / Oki, H. / Yoshida, T. / Ohkubo, T. / Koide, T. / Kobayashi, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Spatiotemporal regulation of PEDF signaling by type I collagen remodeling.
Authors: Kawahara, K. / Yoshida, T. / Maruno, T. / Oki, H. / Ohkubo, T. / Koide, T. / Kobayashi, Y.
History
DepositionJan 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pigment epithelium-derived factor
F: Collagen model peptide, type I, alpha 2
G: Collagen model peptide, type I, alpha 1
H: Collagen model peptide, type I, alpha 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0497
Polymers51,7614
Non-polymers2883
Water1,47782
1
A: Pigment epithelium-derived factor
hetero molecules

F: Collagen model peptide, type I, alpha 2
G: Collagen model peptide, type I, alpha 1
H: Collagen model peptide, type I, alpha 1


Theoretical massNumber of molelcules
Total (without water)52,0497
Polymers51,7614
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1/2,-y-1/2,z+1/21
Buried area5620 Å2
ΔGint-62 kcal/mol
Surface area21790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.378, 147.773, 91.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11F-105-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pigment epithelium-derived factor / PEDF / Caspin / Serpin F1 / Stromal cell-derived factor 3 / SDF-3


Mass: 42300.430 Da / Num. of mol.: 1 / Mutation: P374, P378, L381 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Serpinf1, Pedf, Sdf3 / Production host: Escherichia coli (E. coli) / References: UniProt: P97298

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Collagen model peptide, type I, alpha ... , 3 types, 3 molecules FGH

#2: Protein/peptide Collagen model peptide, type I, alpha 2


Mass: 3258.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein/peptide Collagen model peptide, type I, alpha 1


Mass: 3152.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Protein/peptide Collagen model peptide, type I, alpha 1


Mass: 3049.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 85 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 90 mM CAPS pH 10.5, 1080 mM Sodium phosphate, 720 mM Potassium phosphate and 180 mM Lithium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 22356 / % possible obs: 95.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.046 / Rrim(I) all: 0.124 / Χ2: 1.382 / Net I/σ(I): 6.7 / Num. measured all: 157108
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.47-2.515.70.8578760.8830.3660.9340.77675.3
2.51-2.566.10.8059140.8920.3310.8720.79781.1
2.56-2.616.30.6759370.9270.2770.7310.79581.3
2.61-2.666.40.68410100.9160.2810.7410.82886.4
2.66-2.726.60.61710470.9350.2510.6680.84391.4
2.72-2.786.80.63810970.9270.2570.6890.85695.5
2.78-2.8570.52811510.9470.2120.570.8999.1
2.85-2.937.30.50611800.960.2010.5450.936100
2.93-3.017.50.38511410.9770.1510.4141100
3.01-3.117.50.33211470.9840.130.3561.054100
3.11-3.227.40.26311640.9860.1030.2831.131100
3.22-3.357.50.20411690.990.080.2191.21100
3.35-3.57.40.1511660.9940.0590.1611.339100
3.5-3.697.40.12411680.9950.0490.1341.525100
3.69-3.927.40.111600.9970.040.1081.668100
3.92-4.227.30.08711950.9960.0350.0941.914100
4.22-4.657.20.08511620.9970.0340.0912.643100
4.65-5.327.10.07611980.9960.0310.0832.629100
5.32-6.77.20.06212060.9970.0250.0671.816100
6.7-506.70.04412680.9980.0180.0481.98599.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IMV

1imv


Resolution: 2.476→47.689 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.33
RfactorNum. reflection% reflection
Rfree0.2821 1997 8.97 %
Rwork0.2229 --
obs0.2282 22268 95.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.84 Å2 / Biso mean: 66.9135 Å2 / Biso min: 38.76 Å2
Refinement stepCycle: final / Resolution: 2.476→47.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 15 82 3536
Biso mean--85.15 63.75 -
Num. residues----447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4761-2.53810.49341120.396112675
2.5381-2.60670.41131180.319119180
2.6067-2.68340.38661290.302129486
2.6834-2.770.37291370.2992140093
2.77-2.8690.33031450.3075147899
2.869-2.98380.32361480.2894149899
2.9838-3.11960.34031450.27931489100
3.1196-3.2840.36121510.24671527100
3.284-3.48970.32791480.2241508100
3.4897-3.75910.28481500.20021513100
3.7591-4.13720.25051500.19121535100
4.1372-4.73540.24411510.16761535100
4.7354-5.96430.22331530.18931552100
5.9643-47.6890.24441600.21921625100

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