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- PDB-1f32: CRYSTAL STRUCTURE OF ASCARIS PEPSIN INHIBITOR-3 -

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Basic information

Entry
Database: PDB / ID: 1f32
TitleCRYSTAL STRUCTURE OF ASCARIS PEPSIN INHIBITOR-3
ComponentsMAJOR PEPSIN INHIBITOR PI-3
KeywordsHYDROLASE INHIBITOR / proteinase inhibitor
Function / homology
Function and homology information


aspartic-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Pepsin inhibitor-3 / Pepsin inhibitor-3-like repeated domain / Pepsin inhibitor-3 domain superfamily / : / Pepsin inhibitor-3-like repeated domain / Arylsulfatase, C-terminal domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major pepsin inhibitor 3
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsNg, K.K. / Petersen, J.F. / Cherney, M.M. / Garen, C. / James, M.N.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structural basis for the inhibition of porcine pepsin by Ascaris pepsin inhibitor-3.
Authors: Ng, K.K. / Petersen, J.F. / Cherney, M.M. / Garen, C. / Zalatoris, J.J. / Rao-Naik, C. / Dunn, B.M. / Martzen, M.R. / Peanasky, R.J. / James, M.N.
History
DepositionMay 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAJOR PEPSIN INHIBITOR PI-3


Theoretical massNumber of molelcules
Total (without water)16,4121
Polymers16,4121
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.455, 72.717, 31.137
Angle α, β, γ (deg.)90.00, 101.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MAJOR PEPSIN INHIBITOR PI-3


Mass: 16411.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascaris suum (pig roundworm) / Plasmid: PET-3D / Production host: Escherichia coli (E. coli) / References: UniProt: P19400
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, potassium fluoride, spermidine-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
225 %(w/v)PEG40001drop
310 mM1dropKF
43 mMspermidine-HCl1drop
51 mM2-mercaptoethanol1drop
630 %(w/v)PEG40001reservoir
72 mM2-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030B / Detector: IMAGE PLATE / Date: Oct 3, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 13394 / Num. obs: 13394 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.263 / Num. unique all: 644 / % possible all: 97.6
Reflection
*PLUS
Num. measured all: 42096
Reflection shell
*PLUS
% possible obs: 97.4 % / Num. unique obs: 726 / Num. measured obs: 1796 / Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementResolution: 1.75→19.58 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 578945.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1362 10.2 %RANDOM
Rwork0.211 ---
all-13394 --
obs-13394 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.74 Å2 / ksol: 0.431 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.76 Å20 Å20.99 Å2
2---2.71 Å20 Å2
3----3.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.75→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms995 0 0 136 1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it2.382
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 200 9.2 %
Rwork0.291 1985 -
obs--98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_PI3.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.327 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.291

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