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- PDB-1j3l: Structure of the RNA-processing inhibitor RraA from Thermus therm... -

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Basic information

Entry
Database: PDB / ID: 1j3l
TitleStructure of the RNA-processing inhibitor RraA from Thermus thermophilis
ComponentsDemethylmenaquinone Methyltransferase
KeywordsTRANSFERASE / Vitamine K2 / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


4-hydroxy-4-methyl-2-oxoglutarate aldolase / 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity / oxaloacetate decarboxylase / ribonuclease inhibitor activity / oxaloacetate decarboxylase activity / regulation of RNA metabolic process / metal ion binding
Similarity search - Function
Regulator of ribonuclease activity A / Ribonuclease E inhibitor RraA/RraA-like / Ribonuclease E inhibitor RraA/RraA-like protein / Ribonuclease E inhibitor RraA/RraA-like superfamily / Aldolase/RraA / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-hydroxy-4-methyl-2-oxoglutarate aldolase / 4-hydroxy-4-methyl-2-oxoglutarate aldolase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsRehse, P.H. / Miyano, M. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the RNA-processing inhibitor RraA from Thermus thermophilis.
Authors: Rehse, P.H. / Kuroishi, C. / Tahirov, T.H.
History
DepositionFeb 4, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Demethylmenaquinone Methyltransferase
B: Demethylmenaquinone Methyltransferase
C: Demethylmenaquinone Methyltransferase
D: Demethylmenaquinone Methyltransferase
E: Demethylmenaquinone Methyltransferase
F: Demethylmenaquinone Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8369
Polymers104,7416
Non-polymers953
Water7,170398
1
A: Demethylmenaquinone Methyltransferase
B: Demethylmenaquinone Methyltransferase
C: Demethylmenaquinone Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4666
Polymers52,3713
Non-polymers953
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Demethylmenaquinone Methyltransferase
E: Demethylmenaquinone Methyltransferase
F: Demethylmenaquinone Methyltransferase


Theoretical massNumber of molelcules
Total (without water)52,3713
Polymers52,3713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.872, 109.068, 270.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1053-

HOH

21C-228-

HOH

DetailsThe biological assembly is a trimer, two of which are in the assymetric unit. Trimer 1 is made up of Chains A,B and C, Trimer 2 is made up of chains D, E and F.

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Components

#1: Protein
Demethylmenaquinone Methyltransferase


Mass: 17456.850 Da / Num. of mol.: 6 / Mutation: L80R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HD8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli)
References: UniProt: P83846, UniProt: Q5SIP7*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.12 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: PEG 1000, magnesium chloride, Tris-Cl, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris-HCl1reservoirpH8.3
250 mM1reservoirMgCl2
329 %PEG10001reservoir
450 mMsodium phosphate1droppH7.0
51.05-0 Mammonium sulfate1drop
620 mMTris-HCl1drop
750 mM1droppH8.0NaCl
820.0 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97900, 0.97925, 0.97000
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 9, 2002
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979251
30.971
ReflectionResolution: 2.3→38.5 Å / Num. all: 193179 / Num. obs: 191090 / % possible obs: 98.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.05 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 15.96
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.32 / Num. unique all: 3762 / % possible all: 92.3
Reflection
*PLUS
% possible obs: 90.8 % / Redundancy: 5.1 %
Reflection shell
*PLUS
% possible obs: 92.3 % / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→38.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 231118.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The following residues have been built into weak density and therefore should be interpretted with caution: A1, B160-164, C159-161, D158-163, E158-161 and F154:157
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3996 6 %RANDOM
Rwork0.206 ---
all0.21 66983 --
obs0.21 66983 85.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.209 Å2 / ksol: 0.29942 e/Å3
Displacement parametersBiso mean: 49.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---3.2 Å20 Å2
3---3.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7291 0 3 398 7692
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it4.561.5
X-RAY DIFFRACTIONc_mcangle_it6.012
X-RAY DIFFRACTIONc_scbond_it6.72
X-RAY DIFFRACTIONc_scangle_it8.392.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 709 6.6 %
Rwork0.277 10097 -
obs--82.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 38.5 Å / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.323

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