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- PDB-1imv: 2.85 A crystal structure of PEDF -

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Basic information

Entry
Database: PDB / ID: 1imv
Title2.85 A crystal structure of PEDF
ComponentsPIGMENT EPITHELIUM-DERIVED FACTOR
KeywordsSIGNALING PROTEIN / serpin / PEDF / 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 / epithelial cell proliferation involved in prostate gland development / axon hillock / response to acidic pH / response to arsenic-containing substance / ovulation cycle / negative regulation of endothelial cell migration ...cellular response to cobalt ion / response to peptide / negative regulation of epithelial cell proliferation involved in prostate gland development / short-term memory / epithelial cell proliferation involved in prostate gland development / axon hillock / response to acidic pH / response to arsenic-containing substance / ovulation cycle / negative regulation of endothelial cell migration / positive regulation of neurogenesis / basement membrane / cellular response to retinoic acid / cellular response to dexamethasone stimulus / negative regulation of angiogenesis / kidney development / cellular response to glucose stimulus / serine-type endopeptidase inhibitor activity / positive regulation of neuron projection development / melanosome / retina development in camera-type eye / collagen-containing extracellular matrix / negative regulation of gene expression / perinuclear region of cytoplasm / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Pigment epithelium derived factor, serpin domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain ...Pigment epithelium derived factor, serpin domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / 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 / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Pigment epithelium-derived factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSimonovic, M. / Gettins, P.G.W. / Volz, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of human PEDF, a potent anti-angiogenic and neurite growth-promoting factor.
Authors: Simonovic, M. / Gettins, P.G. / Volz, K.
History
DepositionMay 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PIGMENT EPITHELIUM-DERIVED FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5502
Polymers44,3291
Non-polymers2211
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.174, 62.514, 45.406
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 PIGMENT EPITHELIUM-DERIVED FACTOR / PEDF


Mass: 44328.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMA / Cell line (production host): BHK / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P36955
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.2M ammonium fluoride, 20% PEG 3350, pH 6.20, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 58 %
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 mg/mlprotein1drop
20.2 Mammonium fluoride1reservoir
320 %PEG33501reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
32981
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
ROTATING ANODERIGAKU RU20021.5418
ROTATING ANODERIGAKU RU20031.5418
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IIC1IMAGE PLATEApr 6, 2001focusing mirrors
RIGAKU RAXIS IIC2IMAGE PLATEApr 8, 2001focusing mirrors
RIGAKU RAXIS IIC3IMAGE PLATEApr 10, 2001focusing mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Ni FILTER + mirrorsSINGLE WAVELENGTHMx-ray1
2Ni FILTER + mirrorsSINGLE WAVELENGTHMx-ray1
3Ni FILTER + mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→36.74 Å / Num. all: 11214 / Num. obs: 11214 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.5
Reflection shellResolution: 2.85→3.03 Å / Redundancy: 3 % / Rmerge(I) obs: 0.37 / Num. unique all: 1166 / % possible all: 65.4
Reflection
*PLUS
Num. measured all: 152138
Reflection shell
*PLUS
% possible obs: 65.4 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QLP

1qlp


Resolution: 2.85→36.74 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 200608.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Residues 1-15 and 353-360 are missing/disordered. The side chains of the following residues are disordered: THR16, ARG79, LYS126, LYS127, ARG174, LYS177, GLU178, ASP181, GLU182, LYS228, THR352.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1167 10.4 %RANDOM
Rwork0.188 ---
all-11241 --
obs-11241 91.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.78 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.92 Å20 Å20 Å2
2--7.44 Å20 Å2
3----3.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.85→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2923 0 14 45 2982
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 140 10.7 %
Rwork0.301 1166 -
obs-1166 65.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMCARBOHYDRATE.PARAM
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMWATER.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.4 % / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.34 / % reflection Rfree: 10.7 % / Rfactor Rwork: 0.301

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