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- PDB-6cj7: Crystal structure of Manduca sexta Serine protease inhibitor (Ser... -

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Basic information

Entry
Database: PDB / ID: 6cj7
TitleCrystal structure of Manduca sexta Serine protease inhibitor (Serpin)-12
ComponentsSerpin-12
KeywordsHYDROLASE INHIBITOR / Serine protease inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function
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
Biological speciesManduca sexta (tobacco hornworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGulati, M. / Hu, Y. / Peng, S. / Pathak, P.K. / Wang, Y. / Deng, J. / Jiang, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM58634 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI112662 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI133589 United States
CitationJournal: Insect Biochem. Mol. Biol. / Year: 2018
Title: Manduca sexta serpin-12 controls the prophenoloxidase activation system in larval hemolymph.
Authors: Yang, F. / Wang, Y. / Sumathipala, N. / Cao, X. / Kanost, M.R. / Jiang, H.
History
DepositionFeb 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serpin-12


Theoretical massNumber of molelcules
Total (without water)43,0251
Polymers43,0251
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.997, 80.555, 55.125
Angle α, β, γ (deg.)90.00, 102.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serpin-12


Mass: 43025.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Manduca sexta (tobacco hornworm)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A3B6UET4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20%PEG 8k 100mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97914 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 45917 / % possible obs: 99 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 29.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.045 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 4435 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DY0

4dy0


Resolution: 1.6→35.819 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1863 1934 4.35 %
Rwork0.1628 --
obs0.1638 44443 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→35.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 0 252 3033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072843
X-RAY DIFFRACTIONf_angle_d0.8973851
X-RAY DIFFRACTIONf_dihedral_angle_d13.8961742
X-RAY DIFFRACTIONf_chiral_restr0.055439
X-RAY DIFFRACTIONf_plane_restr0.005500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.24371230.21432744X-RAY DIFFRACTION87
1.64-1.68440.2631280.20792833X-RAY DIFFRACTION91
1.6844-1.73390.24031350.19972933X-RAY DIFFRACTION93
1.7339-1.78990.27581360.18522935X-RAY DIFFRACTION94
1.7899-1.85390.19591390.18053005X-RAY DIFFRACTION96
1.8539-1.92810.19031360.17473051X-RAY DIFFRACTION98
1.9281-2.01580.21041400.16663083X-RAY DIFFRACTION98
2.0158-2.12210.19211430.16693114X-RAY DIFFRACTION99
2.1221-2.2550.19551390.16433093X-RAY DIFFRACTION98
2.255-2.42910.20131420.17583111X-RAY DIFFRACTION100
2.4291-2.67350.20411420.1783142X-RAY DIFFRACTION100
2.6735-3.06020.20941430.16693129X-RAY DIFFRACTION99
3.0602-3.85480.1621440.14983153X-RAY DIFFRACTION100
3.8548-35.82760.15431440.14433183X-RAY DIFFRACTION99
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)
11.0275-1.32930.17294.5927-2.09182.71970.022-0.0081-0.0339-0.23480.05-0.07250.0913-0.0711-0.05840.1859-0.0129-0.01550.1762-0.01260.191211.174643.900411.6585
21.4338-1.7908-0.35335.6510.15910.7011-0.0763-0.00930.14580.23520.0403-0.5125-0.08430.1614-0.01170.21850.0186-0.05540.2407-0.0070.23717.113341.191422.9216
30.87220.73160.32347.1893-1.02161.3284-0.0814-0.2278-0.04440.64130.24180.1563-0.1042-0.0363-0.14040.21350.05630.03760.25020.01330.14313.894342.386428.077
42.4980.7811-0.09954.06930.24751.4488-0.00690.210.1530.04720.15840.49880.0481-0.2472-0.140.15120.01920.02140.23810.0730.2422-6.542937.784320.9341
50.6668-0.14860.36512.5835-0.80891.8309-0.05080.09490.0934-0.3109-0.0220.1966-0.36520.02460.05910.26580.0149-0.07020.18240.00410.2413-0.160161.19527.1142
62.32780.22141.1082.7388-0.3242.0633-0.04190.19010.0196-0.54940.0186-0.2401-0.36010.20490.05910.4047-0.03640.00170.1913-0.02090.24968.691368.20541.6677
70.7056-0.10950.09523.0776-0.43570.8758-0.01520.01350.0217-0.37810.0338-0.1921-0.04230.1278-0.01090.211-0.0137-0.01550.2076-0.01590.164310.553449.41779.8879
81.4578-0.84520.12672.9145-0.60641.80720.01420.10420.2957-0.31170.0610.0598-0.39360.0931-0.04420.296-0.041-0.03140.1748-0.00390.164.496563.13935.2303
92.6349-0.27082.53532.3606-0.2674.11140.0689-0.0302-0.048-0.22260.0550.0659-0.0334-0.0803-0.10150.2354-0.0082-0.01850.1712-0.00270.18756.743855.3418.3409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 106 )
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 152 )
5X-RAY DIFFRACTION5chain 'A' and (resid 153 through 185 )
6X-RAY DIFFRACTION6chain 'A' and (resid 186 through 206 )
7X-RAY DIFFRACTION7chain 'A' and (resid 207 through 304 )
8X-RAY DIFFRACTION8chain 'A' and (resid 305 through 346 )
9X-RAY DIFFRACTION9chain 'A' and (resid 347 through 373 )

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