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- PDB-9j3p: Human Pigment Epithelium-Derived Factor with Zinc Ions Crystalliz... -

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Basic information

Entry
Database: PDB / ID: 9j3p
TitleHuman Pigment Epithelium-Derived Factor with Zinc Ions Crystallized in P2(1)2(1)2(1) Space Group
ComponentsPigment epithelium-derived factor
KeywordsSIGNALING PROTEIN / metal-binding protein / neurotrophic factor / anti-tumorigenic factor
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 / axon hillock / epithelial cell proliferation involved in prostate gland development / response to arsenic-containing substance / response to acidic pH / negative regulation of endothelial cell migration / ovulation cycle ...cellular response to cobalt ion / response to peptide / negative regulation of epithelial cell proliferation involved in prostate gland development / short-term memory / axon hillock / epithelial cell proliferation involved in prostate gland development / response to arsenic-containing substance / response to acidic pH / negative regulation of endothelial cell migration / ovulation cycle / positive regulation of neurogenesis / basement membrane / cellular response to retinoic acid / cellular response to dexamethasone stimulus / negative regulation of angiogenesis / kidney development / serine-type endopeptidase inhibitor activity / cellular response to glucose stimulus / positive regulation of neuron projection development / melanosome / retina development in camera-type eye / : / negative regulation of gene expression / perinuclear region of cytoplasm / extracellular space / extracellular exosome / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBelousov, A.S. / Chistyakov, D.V. / Baksheeva, V.E. / Bulgakov, T.K. / Bukhdruker, S.S. / Zamyatnin, A.A. / Zinchenko, D.V. / Tsvetkov, P.O. / Permyakov, S.E. / Zernii, E.Y. / Borshchevskiy, V.I.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation21-15-00123 Russian Federation
CitationJournal: To Be Published
Title: Zinc-mediated mechanism of neurodegeneration in glaucoma: a role of pigment epithelium-derived factor
Authors: Chistyakov, D.V. / Shevelyova, M.P. / Iomdina, E.N. / Baksheeva, V.E. / Wu, L. / Shebardina, N.G. / Moysenovich, A.M. / Bulgakov, T.K. / Petrov, S.Y. / Tiulina, V.V. / Pogodina, E.I. / ...Authors: Chistyakov, D.V. / Shevelyova, M.P. / Iomdina, E.N. / Baksheeva, V.E. / Wu, L. / Shebardina, N.G. / Moysenovich, A.M. / Bulgakov, T.K. / Petrov, S.Y. / Tiulina, V.V. / Pogodina, E.I. / Gancharova, O.S. / Belousov, A.S. / Filippova, O.M. / Baldin, A.V. / Goriainov, S.V. / Nikolskaya, A.I. / Zalevsky, A.O. / Deviatkin, A.A. / Vologzhannikova, A.A. / Gorokhovets, N.V. / Litus, E.A. / Zamyatnin, A.A. / Komarov, S.V. / Devred, F. / Sergeeva, M.G. / Zamyatnin Jr, A.A. / Senin, I.I. / Zinchenko, D.V. / Tsvetkov, P.O. / Borshchevskiy, V.I. / Permyakov, S.E. / Zernii, E.Y.
History
DepositionAug 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pigment epithelium-derived factor
B: Pigment epithelium-derived factor
C: Pigment epithelium-derived factor
D: Pigment epithelium-derived factor
E: Pigment epithelium-derived factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,72128
Polymers221,5575
Non-polymers2,16323
Water11,854658
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.234, 131.567, 227.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Pigment epithelium-derived factor / PEDF / Cell proliferation-inducing gene 35 protein / EPC-1 / Serpin F1


Mass: 44311.465 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINF1, PEDF, PIG35 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P36955
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 51.01 % / Description: Diamond-shaped crystals of about 100 um.
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium sulfate, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.23984 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23984 Å / Relative weight: 1
ReflectionResolution: 2.1→19.95 Å / Num. obs: 129458 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 52.41 Å2 / CC1/2: 0.999 / Net I/σ(I): 6.85
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 0.26 / Num. unique obs: 18717 / CC1/2: 0.11 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.95 Å / SU ML: 0.4003 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.9613
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2514 12480 5.09 %
Rwork0.217 232745 -
obs0.2187 129458 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.28 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14487 0 99 658 15244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002915014
X-RAY DIFFRACTIONf_angle_d0.611920397
X-RAY DIFFRACTIONf_chiral_restr0.04262388
X-RAY DIFFRACTIONf_plane_restr0.00432579
X-RAY DIFFRACTIONf_dihedral_angle_d12.08645614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.45982950.4545415X-RAY DIFFRACTION67.53
2.12-2.150.43242840.44275866X-RAY DIFFRACTION74.49
2.15-2.170.42464680.42667442X-RAY DIFFRACTION93.63
2.17-2.20.40194160.41577679X-RAY DIFFRACTION97.31
2.2-2.230.37934440.4087713X-RAY DIFFRACTION97.14
2.23-2.260.45194050.42317888X-RAY DIFFRACTION99.07
2.26-2.290.34764120.37377915X-RAY DIFFRACTION99.57
2.29-2.330.36314040.35527977X-RAY DIFFRACTION99.81
2.33-2.360.3484320.34447918X-RAY DIFFRACTION99.96
2.36-2.40.33824700.33937939X-RAY DIFFRACTION99.94
2.4-2.440.34254090.32817941X-RAY DIFFRACTION99.8
2.44-2.490.31954470.31897950X-RAY DIFFRACTION99.87
2.49-2.540.34074640.31577880X-RAY DIFFRACTION99.96
2.54-2.590.31873880.29687925X-RAY DIFFRACTION99.89
2.59-2.640.32074720.2857982X-RAY DIFFRACTION99.86
2.64-2.710.29254190.27347893X-RAY DIFFRACTION99.87
2.71-2.770.28934630.27097944X-RAY DIFFRACTION100
2.77-2.850.32044630.27127990X-RAY DIFFRACTION99.89
2.85-2.930.31334420.2677827X-RAY DIFFRACTION99.96
2.93-3.030.29944340.25747949X-RAY DIFFRACTION99.99
3.03-3.130.28884040.2497969X-RAY DIFFRACTION99.98
3.13-3.260.25434010.23467967X-RAY DIFFRACTION99.96
3.26-3.410.27914110.22397965X-RAY DIFFRACTION100
3.41-3.590.273850.20518010X-RAY DIFFRACTION100
3.59-3.810.20954110.1927934X-RAY DIFFRACTION100
3.81-4.10.22554050.17368014X-RAY DIFFRACTION100
4.1-4.510.18854130.15257953X-RAY DIFFRACTION99.99
4.51-5.150.17933650.14198013X-RAY DIFFRACTION99.95
5.15-6.450.18694500.1697893X-RAY DIFFRACTION100
6.45-19.950.19414040.15977994X-RAY DIFFRACTION99.83

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