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- PDB-3pis: Crystal Structure of Carcinoscorpius rotundicauda Serine Protease... -

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Basic information

Entry
Database: PDB / ID: 3pis
TitleCrystal Structure of Carcinoscorpius rotundicauda Serine Protease Inhibitor Domain 1
ComponentsKazal-type serine protease inhibitor SPI-1
KeywordsHYDROLASE INHIBITOR / typical non-classical Kazal type inhibitor Fold / serine protease inhibitors (uncharacterized)
Function / homologyKazal-type serine protease inhibitor domain / Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Kazal-type serine protease inhibitor SPI-1
Function and homology information
Biological speciesCarcinoscorpius rotundicauda (Southeast Asian horseshoe crab)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsGiri, P.K. / Tang, X.H. / Sivaraman, J.
CitationJournal: To be Published
Title: Modifying the Substrate Specificity of Carcinoscorpius rotundicauda Serine Protease Inhibitor Domain 1 to Target Thrombin
Authors: Giri, P.K. / Tang, X.H. / Thangamani, S. / Shenoy, R.T. / Ding, J.L. / Swaminathan, K. / Sivaraman, J.
History
DepositionNov 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Kazal-type serine protease inhibitor SPI-1
A: Kazal-type serine protease inhibitor SPI-1


Theoretical massNumber of molelcules
Total (without water)9,2102
Polymers9,2102
Non-polymers00
Water99155
1
D: Kazal-type serine protease inhibitor SPI-1


Theoretical massNumber of molelcules
Total (without water)4,6051
Polymers4,6051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Kazal-type serine protease inhibitor SPI-1


Theoretical massNumber of molelcules
Total (without water)4,6051
Polymers4,6051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.480, 37.214, 36.500
Angle α, β, γ (deg.)90.00, 99.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Kazal-type serine protease inhibitor SPI-1


Mass: 4605.021 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-65
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carcinoscorpius rotundicauda (Southeast Asian horseshoe crab)
Gene: SPI-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A1X1V8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.4M mono ammonium dihydrogen sulphate, 0.1M Tris-HCl pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 16, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 4535 / Num. obs: 4535 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Num. unique all: 381 / % possible all: 80.7

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 273 -Random
Rwork0.2147 ---
all0.2227 4648 --
obs0.2227 4488 96.55 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms574 0 0 55 629
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.66
X-RAY DIFFRACTIONc_bond_d0.009

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