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- PDB-4p0o: Cleaved Serpin 42Da -

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Basic information

Entry
Database: PDB / ID: 4p0o
TitleCleaved Serpin 42Da
ComponentsSerine protease inhibitor 4, isoform B
KeywordsHydrolase inhibitor / Serpin 4 / Serpin 42Da / Serine protease inhibtior / neuroserpin
Function / homology
Function and homology information


negative regulation of peptide hormone processing / Intrinsic Pathway of Fibrin Clot Formation / Glucocorticoid biosynthesis / Cargo concentration in the ER / Prednisone ADME / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / COPII-mediated vesicle transport / Platelet degranulation / Neutrophil degranulation ...negative regulation of peptide hormone processing / Intrinsic Pathway of Fibrin Clot Formation / Glucocorticoid biosynthesis / Cargo concentration in the ER / Prednisone ADME / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / COPII-mediated vesicle transport / Platelet degranulation / Neutrophil degranulation / negative regulation of protein processing / cysteine-type endopeptidase inhibitor activity / 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: 1.8 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 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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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
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.220, 109.770, 140.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-481-

HOH

21A-484-

HOH

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Components

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


Mass: 44309.484 Da / Num. of mol.: 1 / Fragment: UNP residues 33-424
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.: 377 / 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: 3.8 Å3/Da / Density % sol: 67.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium phosphate monobasic, 20 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0332
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 62423 / % possible obs: 99.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 7.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.935 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.935 / % possible all: 98.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1593) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→37.057 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1852 3137 5.03 %
Rwork0.1648 --
obs0.1658 62323 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→37.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2946 0 0 377 3323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083007
X-RAY DIFFRACTIONf_angle_d1.0854067
X-RAY DIFFRACTIONf_dihedral_angle_d15.3741116
X-RAY DIFFRACTIONf_chiral_restr0.043458
X-RAY DIFFRACTIONf_plane_restr0.005528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82810.30031280.2962625X-RAY DIFFRACTION98
1.8281-1.85810.30281390.28442639X-RAY DIFFRACTION98
1.8581-1.89010.25251290.25422645X-RAY DIFFRACTION99
1.8901-1.92450.27141350.22782663X-RAY DIFFRACTION99
1.9245-1.96150.20051330.20952653X-RAY DIFFRACTION99
1.9615-2.00160.20381510.20032650X-RAY DIFFRACTION99
2.0016-2.04510.2271440.19142630X-RAY DIFFRACTION99
2.0451-2.09260.1921550.18592673X-RAY DIFFRACTION99
2.0926-2.1450.1911330.18252659X-RAY DIFFRACTION99
2.145-2.2030.18291370.16972700X-RAY DIFFRACTION99
2.203-2.26780.19981410.16532682X-RAY DIFFRACTION100
2.2678-2.3410.17551290.15972694X-RAY DIFFRACTION100
2.341-2.42460.19191590.16572675X-RAY DIFFRACTION100
2.4246-2.52170.1971620.16732657X-RAY DIFFRACTION100
2.5217-2.63640.18861450.16692700X-RAY DIFFRACTION100
2.6364-2.77540.15651640.16582683X-RAY DIFFRACTION100
2.7754-2.94920.231320.16832714X-RAY DIFFRACTION100
2.9492-3.17680.17951470.16372738X-RAY DIFFRACTION100
3.1768-3.49620.1781390.15682723X-RAY DIFFRACTION100
3.4962-4.00160.161340.13052743X-RAY DIFFRACTION100
4.0016-5.03960.13161350.12642784X-RAY DIFFRACTION100
5.0396-37.0650.19841660.16882856X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.816-0.31940.33173.532-2.00631.9162-0.03030.00040.1763-0.07440.13130.099-0.23030.0033-0.01570.1793-0.0071-0.0150.1377-0.00330.246-39.9893-8.2324-17.7184
23.22370.9961-0.21822.3989-0.47520.7302-0.0363-0.14660.17750.073-0.0011-0.06110.03660.17140.03860.18010.01690.01180.1776-0.04910.1511-30.6757-11.2158-13.534
36.42940.5524-1.44361.63940.06762.6467-0.1043-0.4018-0.03350.18170.0354-0.23840.20620.38050.05150.26370.0922-0.01860.25950.00860.1669-23.1241-21.6375-8.2308
42.7191-0.5547-0.79451.43470.37152.4204-0.03470.1133-0.2913-0.1232-0.0169-0.19610.42060.29580.04890.33970.08750.05020.2184-0.01660.2041-24.4946-29.1342-19.1388
51.941-0.10340.24950.8862-0.13151.4509-0.0059-0.1038-0.1311-0.1910.05410.20490.3282-0.254-0.04290.2985-0.0697-0.02330.1191-0.02710.1941-50.2555-25.4788-21.4803
61.4443-0.10930.30233.0542-0.03753.01660.0448-0.0784-0.1030.02040.07050.23980.2473-0.2907-0.09220.1417-0.0899-0.05380.24110.03020.2379-62.1046-18.2136-20.3263
71.61740.14690.5933.1432-0.87193.7829-0.0590.00390.1364-0.20110.00590.2317-0.0047-0.09950.06130.1604-0.0338-0.01820.1769-0.00530.1668-53.961-11.226-18.8754
84.17480.9250.24581.95350.27890.7808-0.15060.3118-0.204-0.1450.04560.21760.2582-0.32730.14050.2838-0.0239-0.04910.20420.04320.1339-53.7553-21.4817-21.3538
93.14690.4480.27651.16580.08861.0363-0.03560.1404-0.0662-0.15490.0359-0.26260.11370.24980.01970.24520.02020.04530.2324-0.03060.1882-27.0725-16.4392-21.7787
104.42540.49331.61852.00330.02141.084-0.01210.0196-0.1919-0.14430.06590.2010.1484-0.2418-0.0730.2238-0.0402-0.02670.1858-0.00480.1677-52.2538-17.5425-21.2291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 5:27)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 28:85)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 86:114)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 115:159)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 160:194)
6X-RAY DIFFRACTION6CHAIN A AND (RESID 195:215)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 216:261)
8X-RAY DIFFRACTION8CHAIN A AND (RESID 262:280)
9X-RAY DIFFRACTION9CHAIN A AND (RESID 281:340)
10X-RAY DIFFRACTION10CHAIN A AND (RESID 341:381)

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