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- PDB-2ab5: bI3 LAGLIDADG Maturase -

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Basic information

Entry
Database: PDB / ID: 2ab5
TitlebI3 LAGLIDADG Maturase
ComponentsmRNA maturase
KeywordsPROTEIN BINDING / maturase / LAGLIDADG endonuclease / group I intron splicing / RNA binding
Function / homology
Function and homology information


mitochondrial mRNA processing / mitochondrial electron transport, ubiquinol to cytochrome c / Group I intron splicing / proton transmembrane transport / mRNA processing / endonuclease activity / mitochondrial inner membrane / electron transfer activity / oxidoreductase activity / mitochondrion / RNA binding
Similarity search - Function
LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / : / Cytochrome b/b6/petB / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. ...LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / : / Cytochrome b/b6/petB / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Roll / Alpha Beta
Similarity search - Domain/homology
Cytochrome b mRNA maturase bI3 / Cytochrome b mRNA maturase bI3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.2 Å
AuthorsLongo, A. / Leonard, C.W. / Bassi, G.S. / Berndt, D. / Krahn, J.M. / Hall, T.M. / Weeks, K.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase
Authors: Longo, A. / Leonard, C.W. / Bassi, G.S. / Berndt, D. / Krahn, J.M. / Hall, T.M. / Weeks, K.M.
History
DepositionJul 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRNA maturase
B: mRNA maturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,24410
Polymers65,4752
Non-polymers7698
Water4,468248
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.600, 80.200, 66.400
Angle α, β, γ (deg.)90.00, 115.50, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit.

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Components

#1: Protein mRNA maturase


Mass: 32737.699 Da / Num. of mol.: 2 / Fragment: N-terminal insertion of MGHHHHH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: cytochrome b intron bi3 / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q36758, UniProt: Q9ZZW7*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.52 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: n-tetradecyl-beta-D-maltoside, PEG MME 5000, Ammonium sulfate, MES, pH 6.5, vapor diffusion, sitting drop, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU RUH3R11.54181.54
20.9791, 0.9795, 0.9714
41.54
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEDec 2, 2001
Quantum 42CCD
RIGAKU RAXIS IV4IMAGE PLATE
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1YALE MIRRORSSINGLE WAVELENGTHMx-ray1
2MADMx-ray1
4SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.541
30.97911
40.97951
50.97141
Reflection
IDNumberRmerge(I) obsΧ2D res high (Å)D res low (Å)% possible obs
1184260.1061.3772.65098.9
2179050.1240.9342.65098.2
3184420.1011.1392.65099.2
4148980.1631.5952.85098.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.65097.810.0662.592
4.455.699.510.0611.8
3.884.4599.510.0651.47
3.533.8899.810.0831.35
3.283.5399.510.111.244
3.083.2899.610.1621.179
2.933.0899.110.21.148
2.82.9399.310.2621.072
2.692.899.110.3331.016
2.62.6996.310.5310.967
5.65098.220.0550.934
4.455.699.720.0590.813
3.884.4599.620.0820.881
3.533.8899.820.0910.942
3.283.5399.620.1381.036
3.083.2899.720.2041.007
2.933.0899.320.2750.997
2.82.9399.420.4780.959
2.692.898.420.4060.868
2.62.6987.620.4870.886
5.6509830.0571.406
4.455.699.530.0591.06
3.884.4599.730.0711.188
3.533.8899.930.0781.183
3.283.5399.630.1111.289
3.083.2899.830.161.15
2.933.0899.230.2111.119
2.82.9399.630.2641.017
2.692.899.230.3461.001
2.62.6997.730.4260.974
6.035095.940.0962.039
4.796.0399.940.1152.13
4.184.7999.940.1231.953
3.84.1899.840.1491.707
3.533.899.840.1591.29
3.323.5399.940.2131.456
3.153.3299.740.2721.281
3.023.1599.940.3361.27
2.93.0299.740.3641.423
2.82.993.740.4231.27
ReflectionResolution: 2.2→50 Å / Num. all: 30022 / Num. obs: 30022 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.082 / Χ2: 1.034 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.28 Å / % possible obs: 94.8 % / Redundancy: 2.51 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.4 / Num. measured obs: 2858 / Χ2: 1.028 / % possible all: 94.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The MAD data was used for phasing and not for refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1440 4.7 %RANDOM
Rwork0.208 ---
all0.211 29230 --
obs0.211 29230 95.2 %-
Solvent computationSolvent model: Flat Model / Bsol: 63.411 Å2 / ksol: 0.3715 e/Å3
Displacement parametersBiso mean: 38.39 Å2
Baniso -1Baniso -2Baniso -3
1--10.715 Å20 Å2-8.014 Å2
2--4.82 Å20 Å2
3---5.896 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 40 248 4582
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007373
X-RAY DIFFRACTIONc_angle_deg1.31764
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4ion.top

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