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- PDB-3jv1: Crystal structure of the Trypanosoma brucei p22 protein -

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Basic information

Entry
Database: PDB / ID: 3jv1
TitleCrystal structure of the Trypanosoma brucei p22 protein
ComponentsP22 protein
KeywordsHYDROLASE / Mam33 family
Function / homology
Function and homology information


RNA modification / mitochondrial matrix
Similarity search - Function
Mitochondrial Matrix Protein; Chain A / Mitochondrial glycoprotein / Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSprehe, M. / Read, L.K. / Schumacher, M.A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure of the Trypanosoma brucei p22 protein, a cytochrome oxidase subunit II-specific RNA-editing accessory factor.
Authors: Sprehe, M. / Fisk, J.C. / McEvoy, S.M. / Read, L.K. / Schumacher, M.A.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Dec 14, 2011Group: Database references
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P22 protein


Theoretical massNumber of molelcules
Total (without water)20,5491
Polymers20,5491
Non-polymers00
Water97354
1
A: P22 protein

A: P22 protein

A: P22 protein


Theoretical massNumber of molelcules
Total (without water)61,6463
Polymers61,6463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area7070 Å2
ΔGint-48 kcal/mol
Surface area26830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.046, 82.046, 51.932
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-228-

HOH

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Components

#1: Protein P22 protein


Mass: 20548.670 Da / Num. of mol.: 1 / Fragment: UNP residues 46 to 227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb927.6.2420 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q584R4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 40% PEG400 0.1M Imidazole, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: 2009 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→29.32 Å / Num. all: 13481 / Num. obs: 13469 / % possible obs: 99.1 % / Observed criterion σ(F): 4.32 / Observed criterion σ(I): 5.48 / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.083
Reflection shellResolution: 2→2.11 Å / % possible all: 98.5

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.3 Å / σ(F): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1378 -RANDOM
Rwork0.221 ---
obs0.225 13462 99.15 %-
all-13585 --
Displacement parametersBiso mean: 45.4776 Å2
Baniso -1Baniso -2Baniso -3
1-1.799 Å20 Å20 Å2
2--1.799 Å20 Å2
3----3.598 Å2
Refinement stepCycle: LAST / Resolution: 2→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 0 54 1500
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_angle_deg1.4

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