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- PDB-5i70: Crystal Structure of plasmepsin IV -

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Basic information

Entry
Database: PDB / ID: 5i70
TitleCrystal Structure of plasmepsin IV
Components
  • Pepstatin APepstatin
  • Plasmepsin IV
KeywordsHYDROLASE/HYDROLASE INHIBITOR / plasmepsin / aspartic protease / malaria / cathepsin D like / 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 / Peptidase A1 domain-containing protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Actinomyces (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAsojo, O.A.
CitationJournal: To Be Published
Title: Crystal Structure of plasmepsin IV
Authors: Asojo, O.A.
History
DepositionFeb 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Data collection
Revision 1.2Sep 27, 2017Group: Data collection / Derived calculations / Structure summary
Category: diffrn_detector / pdbx_molecule_features / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_molecule_features.class / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Plasmepsin IV
A: Plasmepsin IV
C: Pepstatin A
D: Pepstatin A


Theoretical massNumber of molelcules
Total (without water)75,3434
Polymers75,3434
Non-polymers00
Water0
1
B: Plasmepsin IV
D: Pepstatin A


Theoretical massNumber of molelcules
Total (without water)37,6712
Polymers37,6712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-11 kcal/mol
Surface area13650 Å2
MethodPISA
2
A: Plasmepsin IV
C: Pepstatin A


Theoretical massNumber of molelcules
Total (without water)37,6712
Polymers37,6712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-11 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.420, 103.420, 123.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Plasmepsin IV /


Mass: 36985.457 Da / Num. of mol.: 2 / Fragment: UNP residues 122-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 7G8) (eukaryote)
Strain: isolate 7G8 / Gene: PFBG_05102 / Production host: Escherichia coli (E. coli) / References: UniProt: W7FF86
#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.) Actinomyces (bacteria) / References: Pepstatin

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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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.10M sodium phosphate buffer (pH 5.5) and 60% (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3→42.11 Å / Num. obs: 15066 / % possible obs: 95.3 % / Redundancy: 7.1 % / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→19.97 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.82 / Cross valid method: THROUGHOUT / ESU R Free: 0.116
RfactorNum. reflection% reflectionSelection details
Rfree0.29421 929 6.2 %RANDOM
Rwork0.24819 ---
obs0.25122 14043 94.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.088 Å2
Baniso -1Baniso -2Baniso -3
1-5.49 Å20 Å20 Å2
2--5.49 Å20 Å2
3----10.97 Å2
Refinement stepCycle: 1 / Resolution: 3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5054 0 0 0 5054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.025181
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.9727030
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3995632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62625.498231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68815796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.641155
X-RAY DIFFRACTIONr_chiral_restr0.0980.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213918
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1891.9692578
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9782.9263186
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4322.0322602
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.06616.5497550
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 50 -
Rwork0.313 1095 -
obs--100 %

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