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- PDB-2ghu: Crystal structure of falcipain-2 from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 2ghu
TitleCrystal structure of falcipain-2 from Plasmodium falciparum
Componentsfalcipain 2
KeywordsHYDROLASE / papain-like cysteine protease / L-domain / R-domain / alpha helix / random coil / twisted antiparallel beta-sheet
Function / homology
Function and homology information


cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / membrane
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHogg, T. / Nagarajan, K. / Schmidt, C.L. / Hilgenfeld, R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural and Functional Characterization of Falcipain-2, a Hemoglobinase from the Malarial Parasite Plasmodium falciparum.
Authors: Hogg, T. / Nagarajan, K. / Herzberg, S. / Chen, L. / Shen, X. / Jiang, H. / Wecke, M. / Blohmke, C. / Hilgenfeld, R. / Schmidt, C.L.
History
DepositionMar 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: falcipain 2
B: falcipain 2
C: falcipain 2
D: falcipain 2


Theoretical massNumber of molelcules
Total (without water)108,7474
Polymers108,7474
Non-polymers00
Water72140
1
A: falcipain 2


Theoretical massNumber of molelcules
Total (without water)27,1871
Polymers27,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: falcipain 2


Theoretical massNumber of molelcules
Total (without water)27,1871
Polymers27,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: falcipain 2


Theoretical massNumber of molelcules
Total (without water)27,1871
Polymers27,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: falcipain 2


Theoretical massNumber of molelcules
Total (without water)27,1871
Polymers27,1871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.830, 168.280, 178.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is presumed to be a monomer.

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Components

#1: Protein
falcipain 2


Mass: 27186.672 Da / Num. of mol.: 4 / Fragment: Mature wild-type enzyme (residues 1-241)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pQE-30 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9N6S8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 5.02 Å3/Da / Density % sol: 75.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.4-0.8 M ammonium sulfate, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8045 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 20, 2005
RadiationMonochromator: sagitally focused Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8045 Å / Relative weight: 1
ReflectionResolution: 3.04→76.03 Å / Num. obs: 40840 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 52.9 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 11.5
Reflection shellResolution: 3.04→3.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4411 / % possible all: 71.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MIXED MODEL DERIVED FROM PDB ENTRY 1S4V

1s4v


Resolution: 3.1→40 Å / Isotropic thermal model: grouped / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2010 -random
Rwork0.231 ---
all-39960 --
obs-37950 99.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2--2.25 Å20 Å2
3----3.043 Å2
Refinement stepCycle: LAST / Resolution: 3.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7614 0 0 40 7654
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.405 323 -
Rwork0.397 --
obs-6561 100 %

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