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- PDB-1f34: CRYSTAL STRUCTURE OF ASCARIS PEPSIN INHIBITOR-3 BOUND TO PORCINE ... -

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Basic information

Entry
Database: PDB / ID: 1f34
TitleCRYSTAL STRUCTURE OF ASCARIS PEPSIN INHIBITOR-3 BOUND TO PORCINE PEPSIN
Components
  • MAJOR PEPSIN INHIBITOR PI-3
  • PEPSIN A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / proteinase-inhibitor complex / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Surfactant metabolism / pepsin A / aspartic-type endopeptidase inhibitor activity / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular exosome / 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 / Pepsin catalytic domain / Arylsulfatase, C-terminal domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family ...Pepsin inhibitor-3 / Pepsin inhibitor-3-like repeated domain / Pepsin inhibitor-3 domain superfamily / Pepsin inhibitor-3-like repeated domain / Pepsin catalytic domain / Arylsulfatase, C-terminal domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Pepsin A / Major pepsin inhibitor 3
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.45 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPSIN A
B: MAJOR PEPSIN INHIBITOR PI-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1233
Polymers51,0052
Non-polymers1181
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-32 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.374, 97.593, 136.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-381-

HOH

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Components

#1: Protein PEPSIN A


Mass: 34593.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: STOMACH / References: UniProt: P00791, pepsin A
#2: 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
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: PEG 4000, sodium phosphate, 2-methyl-2,4-pentanediol, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlporcine pepsin1drop
25.8 mg/mlPI-31drop
36 %(w/v)PEG40001drop
425 mMsodium phosphate1drop
512 %(w/v)PEG40001reservoir
650 mMsodium phosphate1reservoir
715 %(v/v)MPD1reservoir

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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: Nov 13, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. all: 16263 / Num. obs: 16263 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 24.6
Reflection shellResolution: 2.45→2.48 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.327 / Num. unique all: 442 / % possible all: 78.6
Reflection
*PLUS
Num. measured all: 116274
Reflection shell
*PLUS
% possible obs: 98.9 % / Num. unique obs: 832 / Num. measured obs: 5733 / Mean I/σ(I) obs: 5.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementResolution: 2.45→18.66 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2111863.39 / 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
Rfree0.29 1629 10 %RANDOM
Rwork0.218 ---
obs0.218 16263 99.4 %-
all-16263 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.98 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.28 Å20 Å20 Å2
2---2.95 Å20 Å2
3----3.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.45→18.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 0 110 3617
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.891.5
X-RAY DIFFRACTIONc_mcangle_it3.052
X-RAY DIFFRACTIONc_scbond_it2.732
X-RAY DIFFRACTIONc_scangle_it3.722.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 263 9.9 %
Rwork0.276 2396 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_SEP.PARAMPROTEIN_SEP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.7 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_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
X-RAY DIFFRACTIONc_mcbond_it1.891.5
X-RAY DIFFRACTIONc_scbond_it2.732
X-RAY DIFFRACTIONc_mcangle_it3.052
X-RAY DIFFRACTIONc_scangle_it3.722.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.366 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.276

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