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- PDB-7sap: The CTI-homolog pacifastin -

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Basic information

Entry
Database: PDB / ID: 7sap
TitleThe CTI-homolog pacifastin
ComponentsSerine protease inhibitor I/II-like Protein
KeywordsTOXIN / CTI-homolog / pacifastin / CDP / cystine-dense peptides
Biological speciesTribolium castaneum (red flour beetle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsGewe, M.M. / Strong, R.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Transl Med / Year: 2022
Title: Ex silico engineering of cystine-dense peptides yielding a potent bispecific T cell engager.
Authors: Crook, Z.R. / Girard, E.J. / Sevilla, G.P. / Brusniak, M.Y. / Rupert, P.B. / Friend, D.J. / Gewe, M.M. / Clarke, M. / Lin, I. / Ruff, R. / Pakiam, F. / Phi, T.D. / Bandaranayake, A. / ...Authors: Crook, Z.R. / Girard, E.J. / Sevilla, G.P. / Brusniak, M.Y. / Rupert, P.B. / Friend, D.J. / Gewe, M.M. / Clarke, M. / Lin, I. / Ruff, R. / Pakiam, F. / Phi, T.D. / Bandaranayake, A. / Correnti, C.E. / Mhyre, A.J. / Nairn, N.W. / Strong, R.K. / Olson, J.M.
History
DepositionSep 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease inhibitor I/II-like Protein
B: Serine protease inhibitor I/II-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3844
Polymers7,2002
Non-polymers1842
Water1,11762
1
A: Serine protease inhibitor I/II-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6922
Polymers3,6001
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine protease inhibitor I/II-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6922
Polymers3,6001
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)19.774, 50.502, 25.327
Angle α, β, γ (deg.)90.000, 104.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Serine protease inhibitor I/II-like Protein


Mass: 3600.058 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Production host: Homo sapiens (human)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.7 Å3/Da / Density % sol: 27.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals grew after ~6 months from sparse matrix screen JCSG+ Suite C10 (0.1 M MES pH 6.5, 25 % (w/v) PEG 8000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 11, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.79→25.25 Å / Num. obs: 3164 / % possible obs: 69 % / Redundancy: 3.4 % / Biso Wilson estimate: 15.44 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.044 / Net I/σ(I): 35.66
Reflection shellResolution: 1.79→1.85 Å / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 3.12 / Num. unique obs: 38 / CC1/2: 1 / Rrim(I) all: 0.186

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SAO

7sao


Resolution: 1.79→25.25 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.801 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1875 167 5.3 %RANDOM
Rwork0.1277 ---
obs0.1309 2998 68.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.34 Å2 / Biso mean: 18.644 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0.01 Å2
2--0.05 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.79→25.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms486 0 21 62 569
Biso mean--38.32 29.06 -
Num. residues----66
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.013508
X-RAY DIFFRACTIONr_bond_other_d0.0010.011458
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.691687
X-RAY DIFFRACTIONr_angle_other_deg1.4141.6081048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.117566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.23118.66730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1631577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.348158
X-RAY DIFFRACTIONr_chiral_restr0.0760.274
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02129
LS refinement shellResolution: 1.79→1.834 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rwork0.141 25 -
obs--7.58 %

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