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

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Basic information

Entry
Database: PDB / ID: 7sgq
TitleProtease inhibitors variant, CTI-homolog pacifastin
ComponentsProtease inhibitor LCMI-II
KeywordsTOXIN / CTI / Pacifastin / Protease inhibitors
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: 2.09 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 7, 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 16, 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

Downloads & links

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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
E: Protease inhibitor LCMI-II
F: Protease inhibitor LCMI-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9888
Polymers22,7966
Non-polymers1922
Water75742
1
A: Protease inhibitor LCMI-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8952
Polymers3,7991
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protease inhibitor LCMI-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8952
Polymers3,7991
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protease inhibitor LCMI-II


Theoretical massNumber of molelcules
Total (without water)3,7991
Polymers3,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protease inhibitor LCMI-II


Theoretical massNumber of molelcules
Total (without water)3,7991
Polymers3,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Protease inhibitor LCMI-II


Theoretical massNumber of molelcules
Total (without water)3,7991
Polymers3,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Protease inhibitor LCMI-II


Theoretical massNumber of molelcules
Total (without water)3,7991
Polymers3,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.814, 72.730, 41.235
Angle α, β, γ (deg.)90.000, 123.100, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

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Components

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


Mass: 3799.269 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: LCM_LOCMI - Protease inhibitors variant / Source: (gene. exp.) Locusta migratoria (migratory locust) / Production host: Homo sapiens (human) / References: UniProt: P80060
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.81 Å3/Da / Density % sol: 32.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2M NaCl, 2M (NH4)SO4

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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 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 9376 / % possible obs: 95.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.054 / Rrim(I) all: 0.143 / Χ2: 0.962 / Net I/σ(I): 4.4 / Num. measured all: 62496
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.09-2.132.90.4952940.820.3080.5890.75158.3
2.13-2.163.60.4553690.8560.2560.5260.73378.8
2.16-2.214.50.54510.8440.2520.5630.72792
2.21-2.2550.4114550.9220.1950.4570.71194
2.25-2.35.60.4864750.8960.2170.5340.71797.7
2.3-2.356.20.4064890.9560.1730.4420.7799
2.35-2.416.60.3934870.9590.1630.4260.72799.8
2.41-2.4870.384720.9610.1540.410.76599.8
2.48-2.557.20.344940.9630.1350.3660.793100
2.55-2.637.30.3054770.9760.120.3280.846100
2.63-2.737.40.2784970.9740.1090.2990.873100
2.73-2.847.40.2274740.9890.0890.2440.87100
2.84-2.977.50.184940.9920.070.1930.851100
2.97-3.127.50.1464850.9950.0570.1570.926100
3.12-3.327.50.1264920.9940.0490.1360.976100
3.32-3.577.60.1024800.9970.040.1091.1100
3.57-3.937.50.0934990.9970.0360.11.52100
3.93-4.57.50.0724890.9990.0280.0781.619100
4.5-5.677.50.0644990.9990.0250.0691.115100
2.09-2.1437.30.064550.9990.0240.0651.08299

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kl1

1kl1


Resolution: 2.09→27.58 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.858 / SU B: 9.04 / SU ML: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3222 455 4.9 %RANDOM
Rwork0.2472 ---
obs0.251 8919 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.63 Å2 / Biso mean: 28.86 Å2 / Biso min: 10.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.31 Å2
2---0.3 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 2.09→27.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1373 0 10 42 1425
Biso mean--48.81 30.26 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131448
X-RAY DIFFRACTIONr_bond_other_d0.0010.0111230
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.6781964
X-RAY DIFFRACTIONr_angle_other_deg1.341.6092850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6395204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.38618.15876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.18515209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4031521
X-RAY DIFFRACTIONr_chiral_restr0.0770.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021707
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02343
LS refinement shellResolution: 2.09→2.143 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.29 31 -
Rwork0.317 470 -
obs--68.72 %

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