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- PDB-7slt: Protease inhibitors variant, CTI-homolog pacifastin -

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Basic information

Entry
Database: PDB / ID: 7slt
TitleProtease inhibitors variant, CTI-homolog pacifastin
ComponentsProtease inhibitor LCMI-II
KeywordsTOXIN / CDP / pacifastin / CTI
Function / homologyProtease inhibitor with pacifastin repeats / Pacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / serine-type endopeptidase inhibitor activity / extracellular region / Protease inhibitors
Function and homology information
Biological speciesLocusta migratoria (migratory locust)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionOct 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease inhibitor LCMI-II
B: Protease inhibitor LCMI-II
C: Protease inhibitor LCMI-II
D: Protease inhibitor LCMI-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9577
Polymers14,6804
Non-polymers2763
Water93752
1
A: Protease inhibitor LCMI-II
C: Protease inhibitor LCMI-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4323
Polymers7,3402
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-13 kcal/mol
Surface area4890 Å2
MethodPISA
2
B: Protease inhibitor LCMI-II
D: Protease inhibitor LCMI-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5244
Polymers7,3402
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-11 kcal/mol
Surface area4700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.914, 67.386, 50.369
Angle α, β, γ (deg.)90.000, 108.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide
Protease inhibitor LCMI-II / PARS intercerebralis major peptide C / PMP-C


Mass: 3670.089 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: LCM_LOCMI - Protease inhibitors variant / Source: (gene. exp.) Locusta migratoria (migratory locust) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: P80060
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 33.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 25% (w/v) PEG 8000 / PH range: 6.5

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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: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 7018 / % possible obs: 89.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.043 / Rrim(I) all: 0.113 / Χ2: 1.734 / Net I/σ(I): 8.1 / Num. measured all: 46022
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.982.80.4331520.770.2640.5120.7837.5
1.98-2.023.30.3041890.8990.1760.3550.77149.3
2.02-2.063.70.2892220.9140.1570.3310.88959.4
2.06-2.14.20.2972890.8690.1570.3390.8569.5
2.1-2.1550.3113040.9170.150.3470.87486.4
2.15-2.260.3153920.9450.1370.3440.94798.7
2.2-2.256.60.3043980.9550.1280.3311.00499.3
2.25-2.316.90.2883710.9740.1180.3120.999100
2.31-2.3870.2684030.9710.1090.291.091100
2.38-2.467.10.2313660.9730.0930.2491.209100
2.46-2.547.20.2244070.980.090.2421.192100
2.54-2.657.30.1763840.9790.0710.191.527100
2.65-2.777.30.153940.9870.060.1621.738100
2.77-2.917.30.1623960.9870.0650.1751.82100
2.91-3.17.30.1173740.9920.0480.1272.085100
3.1-3.337.30.0963940.9940.0390.1042.206100
3.33-3.677.30.0843970.9950.0340.0912.47100
3.67-4.27.20.0834040.9960.0330.0892.95100
4.2-5.297.20.0733790.9960.030.0793.162100
5.29-507.10.0594030.9970.0250.0642.55798.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GL1

1gl1


Resolution: 2→28.98 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.279 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 318 4.7 %RANDOM
Rwork0.1971 ---
obs0.1995 6489 93.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.94 Å2 / Biso mean: 34.201 Å2 / Biso min: 17.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.02 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 18 52 976
Biso mean--55.7 40.41 -
Num. residues----131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013946
X-RAY DIFFRACTIONr_bond_other_d0.0020.018811
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.6881275
X-RAY DIFFRACTIONr_angle_other_deg1.3371.6011876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3225129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.0616.66754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57815129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5441517
X-RAY DIFFRACTIONr_chiral_restr0.0650.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02225
LS refinement shellResolution: 2.001→2.053 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 7 -
Rwork0.163 257 -
all-264 -
obs--50.67 %

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