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- PDB-3qvc: Crystal structure of histo-aspartic protease (HAP) zymogen from P... -

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Basic information

Entry
Database: PDB / ID: 3qvc
TitleCrystal structure of histo-aspartic protease (HAP) zymogen from Plasmodium falciparum
ComponentsHisto-aspartic protease
KeywordsHYDROLASE / Histo-aspartic protease / HAP / Plasmepsin / Aspartic protease / Malaria / Zymogen
Function / homology
Function and homology information


plasmepsin II / acquisition of nutrients from host / vacuolar lumen / food vacuole / 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 domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBhaumik, P. / Gustchina, A. / Wlodawer, A.
CitationJournal: Biochemistry / Year: 2011
Title: Structural insights into the activation and inhibition of histo-aspartic protease from Plasmodium falciparum.
Authors: Bhaumik, P. / Xiao, H. / Hidaka, K. / Gustchina, A. / Kiso, Y. / Yada, R.Y. / Wlodawer, A.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histo-aspartic protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0656
Polymers51,7551
Non-polymers3105
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histo-aspartic protease
hetero molecules

A: Histo-aspartic protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,13112
Polymers103,5102
Non-polymers62110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area3040 Å2
ΔGint6 kcal/mol
Surface area33230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.490, 68.430, 72.770
Angle α, β, γ (deg.)90.00, 125.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Histo-aspartic protease / HAP protein / Putative aspartic proteinase


Mass: 51754.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: hap / Plasmid: pET32B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3) pLysS / References: UniProt: Q9Y006
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 20% (w/v) PEG 3350, 0.2M Tri-potassium citrate, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 38417 / Num. obs: 37803 / % possible obs: 98.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.1461 / Mean I/σ(I) obs: 1.2 / % possible all: 97.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36.37 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 12.521 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23936 1410 5 %RANDOM
Rwork0.18351 ---
obs0.1863 26780 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.768 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å2-1.33 Å2
2--2.22 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 0 20 242 3209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223062
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2751.9694143
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8485377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49225.522134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.90615545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.627154
X-RAY DIFFRACTIONr_chiral_restr0.210.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212270
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_it1.0831.51853
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93923025
X-RAY DIFFRACTIONr_scbond_it3.10631209
X-RAY DIFFRACTIONr_scangle_it4.7714.51113
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 102 -
Rwork0.263 1947 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.1858-0.7622-1.05770.37950.13960.87340.04620.23950.161-0.0742-0.03180.0556-0.10660.023-0.01440.0827-0.0058-0.04380.1974-0.00530.05255.619-3.32-24.917
22.08730.14041.02560.977-0.45242.4488-0.11090.11320.0119-0.15730.08370.1035-0.0038-0.25220.02720.0840.0052-0.08640.1361-0.01530.0966-21.1484.159-26.693
31.7234-0.78140.1420.80540.56831.5911-0.05090.0450.0354-0.10760.0292-0.0359-0.19440.14070.02170.1386-0.0147-0.06120.08890.00740.08181.7276.37-13.544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A77P - 8
2X-RAY DIFFRACTION2A9 - 193
3X-RAY DIFFRACTION3A194 - 328

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