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- PDB-1qs8: Crystal structure of the P. vivax aspartic proteinase plasmepsin ... -

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Basic information

Entry
Database: PDB / ID: 1qs8
TitleCrystal structure of the P. vivax aspartic proteinase plasmepsin complexed with the inhibitor pepstatin A
Components
  • PEPSTATIN APepstatin
  • PLASMEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PLASMEPSIN / ASPARTIC PROTEINASE / HAEMOGLOBINASE / MALARIA / PEPSTATIN A / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Pepsin-like domain / 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 ...Pepsin-like domain / 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 / Mainly Beta
Similarity search - Domain/homology
Pepstatin / ACETATE ION / : / (malaria parasite P. vivax) hypothetical protein
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
Streptomyces argenteolus subsp. toyonakensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsKhazanovich Bernstein, N. / Cherney, M.M. / Yowell, C.A. / Dame, J.B. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structural insights into the activation of P. vivax plasmepsin.
Authors: Bernstein, N.K. / Cherney, M.M. / Yowell, C.A. / Dame, J.B. / James, M.N.
History
DepositionJun 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLASMEPSIN
B: PLASMEPSIN
C: PEPSTATIN A
D: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8086
Polymers75,6894
Non-polymers1182
Water2,774154
1
A: PLASMEPSIN
C: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9043
Polymers37,8452
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-12 kcal/mol
Surface area14320 Å2
MethodPISA
2
B: PLASMEPSIN
D: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9043
Polymers37,8452
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-10 kcal/mol
Surface area14170 Å2
MethodPISA
3
A: PLASMEPSIN
C: PEPSTATIN A
hetero molecules

B: PLASMEPSIN
D: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8086
Polymers75,6894
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554y+1/2,-x+1/2,z-1/41
Buried area5480 Å2
ΔGint-47 kcal/mol
Surface area26130 Å2
MethodPISA
4
A: PLASMEPSIN
B: PLASMEPSIN
C: PEPSTATIN A
D: PEPSTATIN A
hetero molecules

A: PLASMEPSIN
B: PLASMEPSIN
C: PEPSTATIN A
D: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,61512
Polymers151,3798
Non-polymers2364
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)145.015, 145.015, 71.072
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PLASMEPSIN /


Mass: 37158.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Production host: Bacteria (eubacteria) / References: GenBank: AAC15792, UniProt: O60989*PLUS
#2: Protein/peptide PEPSTATIN A / Pepstatin /


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 685.891 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Streptomyces argenteolus subsp. toyonakensis (bacteria)
References: Pepstatin
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.51 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG 3000, AMMONIUM SULFATE, ACETATE, AMYL ALCOHOL, BETA-OCTYL GLUCOSIDE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 %(v/v)PEG30001reservoir
20.2 Mammonium sulfate1reservoir
30.1 MNa acetate1reservoir
43 %(v/v)MPD1reservoir
50.15 %(w/v)beta-octylglucoside1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.47→25 Å / Num. all: 27767 / Num. obs: 27347 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.4
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / % possible all: 96.8
Reflection
*PLUS
Num. measured all: 130851
Reflection shell
*PLUS
% possible obs: 97.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementResolution: 2.5→25 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2434582.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1353 5.1 %RANDOM
Rwork0.197 ---
obs0.197 26324 98.4 %-
all-26791 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.63 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1-3.37 Å20 Å20 Å2
2--3.37 Å20 Å2
3----6.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 0 8 154 5472
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.461.5
X-RAY DIFFRACTIONc_mcangle_it3.932
X-RAY DIFFRACTIONc_scbond_it3.812
X-RAY DIFFRACTIONc_scangle_it5.322.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 200 4.7 %
Rwork0.264 4081 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_PEPST_REP.PARAMPROTEIN_PEPST.TOP
X-RAY DIFFRACTION2WATER_REP.PARAACETATE.TOP
X-RAY DIFFRACTION3WATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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