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- PDB-7snd: Pacifastin related protease inhibitors -

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Basic information

Entry
Database: PDB / ID: 7snd
TitlePacifastin related protease inhibitors
ComponentsPacifastin-related peptide
KeywordsTOXIN / CDP / Pacifastin / protease inhibitor
Function / homologyPacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / serine-type endopeptidase inhibitor activity / extracellular region / PHOSPHATE ION / Pacifastin-related peptide
Function and homology information
Biological speciesCoptotermes formosanus (Formosan subterranean termite)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsGewe, M.M. / Strong, R.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: 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.
#1: Journal: Nat Struct Mol Biol / Year: 2018
Title: Screening, large-scale production and structure-based classification of cystine-dense peptides
Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S. ...Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S.M. / May, D. / Watson, A. / Chan, M.K. / Bahl, C.D. / Olson, J.M. / Strong, R.K.
History
DepositionOct 27, 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 1.2Nov 6, 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: Pacifastin-related peptide
B: Pacifastin-related peptide
C: Pacifastin-related peptide
D: Pacifastin-related peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5157
Polymers14,2364
Non-polymers2793
Water1,58588
1
A: Pacifastin-related peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7433
Polymers3,5591
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pacifastin-related peptide


Theoretical massNumber of molelcules
Total (without water)3,5591
Polymers3,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pacifastin-related peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6542
Polymers3,5591
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pacifastin-related peptide


Theoretical massNumber of molelcules
Total (without water)3,5591
Polymers3,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.110, 52.202, 35.101
Angle α, β, γ (deg.)90.000, 101.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Pacifastin-related peptide


Mass: 3558.979 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coptotermes formosanus (Formosan subterranean termite)
Production host: Homo sapiens (human) / References: UniProt: R4UK43
#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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.65 Å3/Da / Density % sol: 25.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium Chloride, 0.1 M Phosphate-Citrate pH 4.2, 20% PEG 1000

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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: Oct 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 6336 / % possible obs: 72.2 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.027 / Rrim(I) all: 0.073 / Χ2: 2.337 / Net I/σ(I): 17.1 / Num. measured all: 45734
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.79-1.823.80.16420.960.0910.1840.9439.8
1.82-1.854.50.128830.9840.0660.1441.28218.3
1.85-1.895.20.136890.990.0640.1511.1320.9
1.89-1.935.80.1211270.9890.0530.1321.5329.7
1.93-1.9760.1171630.9850.0520.1291.59837
1.97-2.026.40.1032030.9960.0440.1131.62945.5
2.02-2.076.80.1032350.9890.0420.1111.80654.1
2.07-2.126.80.1042840.990.0430.1132.268.9
2.12-2.187.20.1014200.9940.0410.1092.2888.8
2.18-2.267.60.1083970.9920.0420.1162.36394.7
2.26-2.347.60.0974340.9910.0370.1042.16396
2.34-2.437.60.0943980.9930.0370.1012.43395
2.43-2.547.60.094210.9940.0350.0972.33695.7
2.54-2.677.60.0824180.9950.0320.0882.41696.5
2.67-2.847.60.0794420.9960.0310.0852.797.1
2.84-3.067.60.0744220.9960.0280.0792.897.2
3.06-3.377.50.0664260.9970.0260.0712.80397.9
3.37-3.867.50.0594360.9980.0230.0632.61298
3.86-4.867.50.0514420.9970.020.0552.52298.7
4.86-507.10.0454540.9990.0180.0491.94498.9

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Processing

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

1gl1


Resolution: 1.79→28.75 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.5 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 322 5.1 %RANDOM
Rwork0.1392 ---
obs0.1424 6003 72.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.99 Å2 / Biso mean: 16.267 Å2 / Biso min: 9.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.02 Å2
2--0.07 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.79→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms964 0 17 88 1069
Biso mean--38.8 25.68 -
Num. residues----131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131008
X-RAY DIFFRACTIONr_bond_other_d0.0020.018850
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.6961365
X-RAY DIFFRACTIONr_angle_other_deg1.3961.5861993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8495131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97820.34558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54915168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9761513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02206
LS refinement shellResolution: 1.791→1.837 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 5 -
Rwork0.165 68 -
all-73 -
obs--11.27 %

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