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- PDB-1n2x: Crystal Structure Analysis of TM0872, a Putative SAM-dependent Me... -

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Basic information

Entry
Database: PDB / ID: 1n2x
TitleCrystal Structure Analysis of TM0872, a Putative SAM-dependent Methyltransferase, Complexed with SAM
ComponentsS-adenosyl-methyltransferase mraW
KeywordsTRANSFERASE / SAM-dependent Methyltransferase Fold / Protein-SAM Methyl Donor Complex / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


16S rRNA (cytosine1402-N4)-methyltransferase / rRNA (cytosine-N4-)-methyltransferase activity / rRNA base methylation / cytoplasm
Similarity search - Function
Putative methyltransferase TM0872, insert domain / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / Vaccinia Virus protein VP39 / DNA polymerase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Putative methyltransferase TM0872, insert domain / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / Vaccinia Virus protein VP39 / DNA polymerase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Ribosomal RNA small subunit methyltransferase H
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMiller, D.J. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2003
Title: Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain
Authors: Miller, D.J. / Ouellette, N. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Anderson, W.F.
History
DepositionOct 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. THE BIOLOGICAL UNIT IS A TRIMER ACCORDING TO DYNAMIC LIGHT SCATTERING DATA.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosyl-methyltransferase mraW
B: S-adenosyl-methyltransferase mraW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7596
Polymers70,7702
Non-polymers9894
Water6,287349
1
A: S-adenosyl-methyltransferase mraW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8793
Polymers35,3851
Non-polymers4952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S-adenosyl-methyltransferase mraW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8793
Polymers35,3851
Non-polymers4952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.960, 133.960, 133.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein S-adenosyl-methyltransferase mraW / TM0872


Mass: 35384.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0872 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3
References: UniProt: Q9WZX6, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: DROP- 50 mM NA CACODYLATE pH 6.5, 5 mM HEPES pH 7.5, 0.1 M AMMONIUM SULFATE, 9 % PEG 8000, 0.25 M NACL, 1.0 MM BME, 10 MG/ML PROTEIN. WELL- 0.1M NA CACODYLATE pH 6.5, 0.1 M AMMONIUM SULFATE, ...Details: DROP- 50 mM NA CACODYLATE pH 6.5, 5 mM HEPES pH 7.5, 0.1 M AMMONIUM SULFATE, 9 % PEG 8000, 0.25 M NACL, 1.0 MM BME, 10 MG/ML PROTEIN. WELL- 0.1M NA CACODYLATE pH 6.5, 0.1 M AMMONIUM SULFATE, 18 % PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMsodium cacodylate1droppH6.5
25 mMHEPES1droppH7.5
30.1 Mammonium sulfate1drop
49 %PEG80001drop
50.25 M1dropNaCl
61 mMbeta-mercaptoethanol1drop
70.3 mMS-adenosyl-L-homocysteine1drop
810 mg/mlprotein1drop
90.1 Msodium cacodylate1reservoirpH6.5
100.2 Mammonium sulfate1reservoir
1118 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9785 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 3, 2002
RadiationMonochromator: Null / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 63197 / Num. obs: 63100 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 25.7 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 29
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 4.65 / Num. unique all: 6264 / % possible all: 99.9
Reflection
*PLUS
Num. obs: 63197 / Num. measured all: 1623397
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 4.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M6Y

1m6y


Resolution: 1.9→19.97 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3187 -RANDOM
Rwork0.205 ---
all0.206 63100 --
obs0.205 63068 99.9 %-
Displacement parametersBiso mean: 40.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-6 Å
Luzzati sigma a0.12 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 64 349 5009
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_scbond_it2.4722
X-RAY DIFFRACTIONc_mcangle_it2.0592
X-RAY DIFFRACTIONc_scangle_it3.7072.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.276 272 -
Rwork0.245 --
obs-5984 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna-multi-endo_rep2.paramdna-rna2.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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