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- PDB-3qrv: Crystal structure of plasmepsin I (PMI) from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 3qrv
TitleCrystal structure of plasmepsin I (PMI) from Plasmodium falciparum
ComponentsPlasmepsin-1
KeywordsHYDROLASE / Aspartic protease / malaria
Function / homology
Function and homology information


plasmepsin I / cytostome / acquisition of nutrients from host / vacuolar lumen / food vacuole / vacuolar membrane / aspartic-type endopeptidase activity / proteolysis
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
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBhaumik, P. / Gustchina, A. / Wlodawer, A.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Crystal structures of the free and inhibited forms of plasmepsin I (PMI) from Plasmodium falciparum.
Authors: Bhaumik, P. / Horimoto, Y. / Xiao, H. / Miura, T. / Hidaka, K. / Kiso, Y. / Wlodawer, A. / Yada, R.Y. / Gustchina, A.
History
DepositionFeb 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 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: Plasmepsin-1
B: Plasmepsin-1


Theoretical massNumber of molelcules
Total (without water)75,6912
Polymers75,6912
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-30 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.170, 93.390, 108.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Plasmepsin-1 / Aspartic hemoglobinase I / PfAPG


Mass: 37845.676 Da / Num. of mol.: 2 / Fragment: UNP residues 117-452
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PMI / Plasmid: pET32b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3) pLysS / References: UniProt: P39898, plasmepsin I
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25% PEG 6000, 0.1M Sodium acetate, pH 4.6, 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: Aug 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 29453 / Num. obs: 29306 / % possible obs: 99.5 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.205 / Net I/σ(I): 9.1
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.1313 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3268 / % possible all: 98.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.895 / SU B: 24.83 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28285 1465 5 %RANDOM
Rwork0.20675 ---
obs0.21057 27830 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: 12.989 Å2
Baniso -1Baniso -2Baniso -3
1--3.65 Å20 Å20 Å2
2--1.36 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5191 0 0 188 5379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225325
X-RAY DIFFRACTIONr_angle_refined_deg2.1861.9527235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6035649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56925.462249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.07915874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.794156
X-RAY DIFFRACTIONr_chiral_restr0.1580.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214050
X-RAY DIFFRACTIONr_mcbond_it0.9821.53235
X-RAY DIFFRACTIONr_mcangle_it1.72725254
X-RAY DIFFRACTIONr_scbond_it2.5132090
X-RAY DIFFRACTIONr_scangle_it3.7894.51981
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 105 -
Rwork0.33 1983 -
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)
11.96490.4541-0.51095.53051.27162.43110.0741-0.13390.2370.3917-0.18310.4865-0.1161-0.01160.1090.4937-0.074-0.06650.0942-0.01110.176329.96620.28138.14
22.24070.86970.95131.76680.03511.74480.0256-0.1611-0.1274-0.02390.0194-0.01990.0953-0.0251-0.0450.47870.00990.02960.02730.0290.114327.0855.79819.183
34.12091.05280.36091.92570.07271.3663-0.0096-0.2819-0.10160.10080.0505-0.2657-0.08020.1615-0.04090.5460.0597-0.02730.0636-0.02080.11360.40736.3039.77
43.0189-2.31081.04993.3288-0.96031.8103-0.004-0.3132-0.16510.15190.1110.1368-0.0353-0.2261-0.1070.4746-0.0413-0.01050.14090.06690.1576-8.05917.09421.339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 190
2X-RAY DIFFRACTION2A191 - 328
3X-RAY DIFFRACTION3B0 - 190
4X-RAY DIFFRACTION4B191 - 328

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