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- PDB-9j3q: Human Pigment Epithelium-Derived Factor with Zinc Ion Crystallize... -

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Basic information

Entry
Database: PDB / ID: 9j3q
TitleHuman Pigment Epithelium-Derived Factor with Zinc Ion Crystallized in P22(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: 1.9 Å
AuthorsBelousov, A.S. / Chistyakov, D.V. / Baksheeva, V.E. / Bulgakov, T.K. / Zamyatnin, A.A. / Zinchenko, D.V. / Wu, L. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,78347
Polymers44,3111
Non-polymers5,47246
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.974, 61.603, 44.796
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,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.: 1
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.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.72 Å3/Da / Density % sol: 54.85 %
Description: Long sticks of 100-200 mm with cross section of 20 mm
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH=8.5, 20 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 1.25 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: May 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 1.9→43.74 Å / Num. obs: 72912 / % possible obs: 99.4 % / Redundancy: 13 % / Biso Wilson estimate: 35.73 Å2 / CC1/2: 0.99 / Net I/σ(I): 35.95
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3819 / CC1/2: 0.37 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XSCALEdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→36.23 Å / SU ML: 0.3427 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.6081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2328 3676 5.04 %
Rwork0.189 69236 -
obs0.1912 72912 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 341 241 3544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793413
X-RAY DIFFRACTIONf_angle_d0.96094505
X-RAY DIFFRACTIONf_chiral_restr0.0573501
X-RAY DIFFRACTIONf_plane_restr0.025544
X-RAY DIFFRACTIONf_dihedral_angle_d17.18251393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.50181100.46952190X-RAY DIFFRACTION81.76
1.93-1.950.4621460.43892542X-RAY DIFFRACTION93.56
1.95-1.980.38081460.39142632X-RAY DIFFRACTION99.14
1.98-2.010.41511380.34232687X-RAY DIFFRACTION99.93
2.01-2.040.34611330.32212694X-RAY DIFFRACTION99.86
2.04-2.070.3421710.30532632X-RAY DIFFRACTION100
2.07-2.110.30591350.29372737X-RAY DIFFRACTION99.97
2.11-2.150.34951530.27552683X-RAY DIFFRACTION100
2.15-2.190.30621440.26452674X-RAY DIFFRACTION100
2.19-2.230.30621490.26872718X-RAY DIFFRACTION100
2.23-2.280.28481320.25732666X-RAY DIFFRACTION100
2.28-2.340.27631090.2172714X-RAY DIFFRACTION100
2.34-2.390.24611500.21662685X-RAY DIFFRACTION99.86
2.39-2.460.23021460.20232740X-RAY DIFFRACTION99.52
2.46-2.530.26341300.1972664X-RAY DIFFRACTION100
2.53-2.610.21991380.18552698X-RAY DIFFRACTION99.93
2.61-2.710.19711310.18122684X-RAY DIFFRACTION99.96
2.71-2.810.2131690.17462702X-RAY DIFFRACTION100
2.81-2.940.23641500.18932680X-RAY DIFFRACTION100
2.94-3.10.23471380.16922671X-RAY DIFFRACTION99.96
3.1-3.290.19451240.16042713X-RAY DIFFRACTION100
3.29-3.540.18491370.1582693X-RAY DIFFRACTION99.96
3.55-3.90.20561500.1512677X-RAY DIFFRACTION99.75
3.9-4.460.21991510.12922717X-RAY DIFFRACTION99.93
4.47-5.620.17071380.13342692X-RAY DIFFRACTION99.89
5.62-36.230.22011580.20012651X-RAY DIFFRACTION99.43
Refinement TLS params.Method: refined / Origin x: -30.248 Å / Origin y: -4.838 Å / Origin z: -10.851 Å
111213212223313233
T0.285977198545 Å2-0.00118959133817 Å20.00953552976064 Å2-0.248817616476 Å20.00123688071835 Å2--0.262341771416 Å2
L1.64362654442 °2-0.118726513863 °20.64804376204 °2-0.309717693115 °2-0.00415389748214 °2--0.799247073877 °2
S0.0314298681081 Å °-0.122166969228 Å °-0.093284830115 Å °-0.0184247090224 Å °0.0470521107972 Å °0.00873713314123 Å °0.0203455331767 Å °0.0365867006632 Å °1.00008468584E-6 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 35:418 OR RESID 501:546 OR RESID 601:841 ) )A35 - 418
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 35:418 OR RESID 501:546 OR RESID 601:841 ) )A501 - 546
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 35:418 OR RESID 501:546 OR RESID 601:841 ) )A601 - 841

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