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- PDB-4afv: THE STRUCTURE OF METACASPASE 2 FROM T. BRUCEI DETERMINED IN THE P... -

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Basic information

Entry
Database: PDB / ID: 4afv
TitleTHE STRUCTURE OF METACASPASE 2 FROM T. BRUCEI DETERMINED IN THE PRESENCE OF CALCIUM CHLORIDE
ComponentsMETACASPASE MCA2
KeywordsHYDROLASE / CYSTEINE PEPTIDASE / CASPASE/HEMOGLOBIN FOLD
Function / homology
Function and homology information


cysteine-type peptidase activity / recycling endosome / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / proteolysis / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / Caspase domain / Caspase-like domain superfamily
Similarity search - Domain/homology
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMcLuskey, K. / Rudolf, J. / Isaacs, N.W. / Coombs, G.H. / Moss, C.X. / Mottram, J.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal Structure of a Trypanosoma Brucei Metacaspase.
Authors: Mcluskey, K. / Rudolf, J. / Proto, W.R. / Isaacs, N.W. / Coombs, G.H. / Moss, C.X. / Mottram, J.C.
History
DepositionJan 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METACASPASE MCA2


Theoretical massNumber of molelcules
Total (without water)39,9581
Polymers39,9581
Non-polymers00
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.600, 49.894, 85.534
Angle α, β, γ (deg.)90.00, 117.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2172-

HOH

21A-2176-

HOH

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Components

#1: Protein METACASPASE MCA2


Mass: 39958.348 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Strain: LISTER 427 / Plasmid: PGL2046 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q585F3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 213 TO ALA
Sequence detailsUNIPROT Q585F3 DIFFERS FROM THIS ENTRY AT POSITION 315 (GLY-ARG). Q585F3 IS THE NEAREST UNIPROT ...UNIPROT Q585F3 DIFFERS FROM THIS ENTRY AT POSITION 315 (GLY-ARG). Q585F3 IS THE NEAREST UNIPROT ENTRY TO MCA2 FROM T. BRUCEI STRAIN 427.

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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: 1.87 Å3/Da / Density % sol: 35 % / Description: NONE
Crystal growpH: 7
Details: 50 MM HEPES PH 7.0, 0.1% TRYPTONE, 20% PEG 3350. CRYSTAL SOAKING FOR 1HR IN 5MM CACL2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2011 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→27.38 Å / Num. obs: 45982 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 6.1 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AF8

4af8


Resolution: 1.5→76.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.246 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-14, 166-171 AND 267-276 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.18452 2316 5 %RANDOM
Rwork0.15243 ---
obs0.15405 43641 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.08 Å / VDW probe radii: 1.4 Å / Solvent model: BULK SOLVENT MODELLING WITH MASK
Displacement parametersBiso mean: 16.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20.18 Å2
2--0.16 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.5→76.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 0 287 2710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222767
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9633801
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64624.72125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07315486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7241517
X-RAY DIFFRACTIONr_chiral_restr0.0860.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212175
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_it1.0631.51750
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82722860
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.52431017
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7974.5922
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.15132767
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 150 -
Rwork0.179 2828 -
obs--85.82 %

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