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- PDB-4p0f: Cleaved Serpin 42Da (C 2 2 21) -

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Basic information

Entry
Database: PDB / ID: 4p0f
TitleCleaved Serpin 42Da (C 2 2 21)
ComponentsSerine protease inhibitor 4, isoform B
KeywordsHYDROLASE INHIBITOR / Serpin 42Da / Serpin 4 / Serine protease inhibitor / neuroserpin / Drosophila
Function / homology
Function and homology information


negative regulation of peptide hormone processing / Intrinsic Pathway of Fibrin Clot Formation / Common Pathway of Fibrin Clot Formation / Glucocorticoid biosynthesis / Peptide ligand-binding receptors / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Prednisone ADME / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Cargo concentration in the ER / Post-translational protein phosphorylation ...negative regulation of peptide hormone processing / Intrinsic Pathway of Fibrin Clot Formation / Common Pathway of Fibrin Clot Formation / Glucocorticoid biosynthesis / Peptide ligand-binding receptors / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Prednisone ADME / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Cargo concentration in the ER / Post-translational protein phosphorylation / G alpha (q) signalling events / G alpha (i) signalling events / COPII-mediated vesicle transport / Platelet degranulation / Metabolism of Angiotensinogen to Angiotensins / Neutrophil degranulation / negative regulation of protein processing / cysteine-type endopeptidase inhibitor activity / regulation of immune response / serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / 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
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEllisdon, A.M. / Whisstock, J.C.
CitationJournal: Bmc Struct.Biol. / Year: 2014
Title: High resolution structure of cleaved Serpin 42 Da from Drosophila melanogaster.
Authors: Ellisdon, A.M. / Zhang, Q. / Henstridge, M.A. / Johnson, T.K. / Warr, C.G. / Law, R.H. / Whisstock, J.C.
History
DepositionFeb 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Data collection
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_oper_list / refine / refine_hist / struct_keywords / symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine.pdbx_diffrn_id / _struct_keywords.text / _symmetry.Int_Tables_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease inhibitor 4, isoform B


Theoretical massNumber of molelcules
Total (without water)44,3091
Polymers44,3091
Non-polymers00
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.740, 125.950, 119.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

21A-479-

HOH

31A-487-

HOH

41A-507-

HOH

51A-510-

HOH

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Components

#1: Protein Serine protease inhibitor 4, isoform B / Serpin 4


Mass: 44309.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Spn42Da, sp4, Spn4, CG9453, Dmel_CG9453 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7K8Y5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium chloride, 20 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→27.88 Å / Num. obs: 50081 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 12.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.672 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1593) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F02

3f02


Resolution: 1.7→27.88 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1882 2542 5.08 %
Rwork0.1656 --
obs0.1667 50043 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→27.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 0 344 3271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062986
X-RAY DIFFRACTIONf_angle_d1.0334035
X-RAY DIFFRACTIONf_dihedral_angle_d13.5781100
X-RAY DIFFRACTIONf_chiral_restr0.039458
X-RAY DIFFRACTIONf_plane_restr0.005519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73270.28031400.2582595X-RAY DIFFRACTION100
1.7327-1.76810.24891590.22562589X-RAY DIFFRACTION100
1.7681-1.80650.25291520.20862606X-RAY DIFFRACTION100
1.8065-1.84850.2271410.19482601X-RAY DIFFRACTION100
1.8485-1.89470.21851330.18522605X-RAY DIFFRACTION100
1.8947-1.94590.21231370.1742627X-RAY DIFFRACTION100
1.9459-2.00320.21591400.17382622X-RAY DIFFRACTION100
2.0032-2.06780.19071320.16792634X-RAY DIFFRACTION100
2.0678-2.14170.20831360.15432623X-RAY DIFFRACTION100
2.1417-2.22740.15761470.15432624X-RAY DIFFRACTION100
2.2274-2.32870.17981490.15942612X-RAY DIFFRACTION100
2.3287-2.45150.19371470.16042627X-RAY DIFFRACTION100
2.4515-2.60490.20481570.16952619X-RAY DIFFRACTION100
2.6049-2.80590.17481190.16482672X-RAY DIFFRACTION100
2.8059-3.08790.1751170.16642673X-RAY DIFFRACTION100
3.0879-3.5340.16621390.15532699X-RAY DIFFRACTION100
3.534-4.44960.15981320.13782696X-RAY DIFFRACTION100
4.4496-27.88210.18851650.17422777X-RAY DIFFRACTION99

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