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- PDB-3tfi: DMSP-dependent demethylase from P. ubique - with substrate DMSP -

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Basic information

Entry
Database: PDB / ID: 3tfi
TitleDMSP-dependent demethylase from P. ubique - with substrate DMSP
ComponentsGcvT-like Aminomethyltransferase protein
KeywordsTRANSFERASE / demethylase / THF
Function / homology
Function and homology information


dimethylsulfoniopropionate demethylase / methyltransferase activity / methylation
Similarity search - Function
Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 / Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain / GCVT N-terminal domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(dimethyl-lambda~4~-sulfanyl)propanoic acid / Dimethylsulfoniopropionate demethylase DmdA
Similarity search - Component
Biological speciesCandidatus Pelagibacter ubique (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchuller, D.J. / Reisch, C.R. / Moran, M.A. / Whitman, W.B. / Lanzilotta, W.N.
CitationJournal: Protein Sci. / Year: 2012
Title: Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagabacter ubique.
Authors: Schuller, D.J. / Reisch, C.R. / Moran, M.A. / Whitman, W.B. / Lanzilotta, W.N.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_asym_id / _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

Downloads & links

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Assembly

Deposited unit
A: GcvT-like Aminomethyltransferase protein
B: GcvT-like Aminomethyltransferase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2768
Polymers83,7732
Non-polymers5036
Water12,196677
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-38 kcal/mol
Surface area29290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.752, 121.992, 59.373
Angle α, β, γ (deg.)90.00, 100.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GcvT-like Aminomethyltransferase protein


Mass: 41886.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gene synthesized with E. coli codon preferences. Plasmid based on pCYB1.
Source: (gene. exp.) Candidatus Pelagibacter ubique (bacteria)
Strain: HTCC1062 / Gene: dmdA, SAR11_0246 / Plasmid: pABX101 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10F' / References: UniProt: Q4FP21, aminomethyltransferase
#2: Chemical ChemComp-DQY / 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid


Mass: 136.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O2S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 298 K / pH: 6.8
Details: 25 mM HEPES, 325 mM NaCl, 20% PEG. PEG increased to 30% for cryo. Soaked with DMSP, pH 6.8, Microbatch under oil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2008 / Details: vertical focusing mirrors
RadiationMonochromator: double crystal Si(111) cooled with lN2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 99295 / Num. obs: 96714 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 21.2 Å2 / Rsym value: 0.08 / Net I/σ(I): 23.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 10 / Num. unique all: 9909 / Rsym value: 0.151 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1WOO, 1V5V

1woo

1v5v


Resolution: 1.6→29.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.843 / SU ML: 0.047 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18407 2369 2.5 %RANDOM
Rwork0.13034 ---
obs0.13164 94015 97.4 %-
all-98946 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.111 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å21.3 Å2
2---0.35 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5898 0 30 677 6605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0226322
X-RAY DIFFRACTIONr_bond_other_d0.0020.024435
X-RAY DIFFRACTIONr_angle_refined_deg1.9681.9618562
X-RAY DIFFRACTIONr_angle_other_deg1.096310916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5285815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.70125.362304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.775151202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1561522
X-RAY DIFFRACTIONr_chiral_restr0.1420.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021251
X-RAY DIFFRACTIONr_mcbond_it2.2871.53790
X-RAY DIFFRACTIONr_mcbond_other0.8221.51550
X-RAY DIFFRACTIONr_mcangle_it3.36226164
X-RAY DIFFRACTIONr_scbond_it4.9432532
X-RAY DIFFRACTIONr_scangle_it6.9874.52360
X-RAY DIFFRACTIONr_rigid_bond_restr2.132310757
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 183 -
Rwork0.102 7084 -
obs-7084 99.36 %

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