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- PDB-4o1f: Structure of a methyltransferase component in complex with THF in... -

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Basic information

Entry
Database: PDB / ID: 4o1f
TitleStructure of a methyltransferase component in complex with THF involved in O-demethylation
ComponentsDihydropteroate synthase DHPS
KeywordsTRANSFERASE / TIM barrel / methyltransferase / THF/MTHF / DCB-2
Function / homology
Function and homology information


pteridine-containing compound metabolic process / methionine synthase activity / methylation / cytosol
Similarity search - Function
: / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
(6S)-5,6,7,8-TETRAHYDROFOLATE / Dihydropteroate synthase DHPS
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSjuts, H. / Dunstan, M.S. / Fisher, K. / Leys, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structures of the methyltransferase component of Desulfitobacterium hafniense DCB-2 O-demethylase shed light on methyltetrahydrofolate formation
Authors: Sjuts, H. / Dunstan, M.S. / Fisher, K. / Leys, D.
History
DepositionDec 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Nov 8, 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 / 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_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

Downloads & links

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Assembly

Deposited unit
A: Dihydropteroate synthase DHPS
B: Dihydropteroate synthase DHPS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4024
Polymers63,5112
Non-polymers8912
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-35 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.190, 118.240, 57.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Dihydropteroate synthase DHPS


Mass: 31755.482 Da / Num. of mol.: 2 / Fragment: UNP residues 2-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: DCB-2 / DSM 10664 / Gene: Dhaf_0722 / Production host: Escherichia coli (E. coli) / References: UniProt: B8FW00
#2: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 277.15 K / pH: 7.5
Details: 100mM Tris pH 7.5, 100mM succinic acid, 15%(v/v) PEG3350, 4mM THF, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 4, 2013
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→30.62 Å / Num. obs: 57921 / % possible obs: 99.8 %
Reflection shellResolution: 1.8→1.847 Å / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O0Q

4o0q


Resolution: 1.8→30.61 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.779 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2902 5 %RANDOM
Rwork0.207 ---
obs0.209 54968 99.8 %-
all-57921 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.73 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4061 0 64 270 4395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194144
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.22625633
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09125.714168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0615713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3331521
X-RAY DIFFRACTIONr_chiral_restr0.2210.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213077
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 192 -
Rwork0.281 4019 -
obs--99.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.29170.3364-0.29291.28880.21771.0044-0.0128-0.0093-0.00210.0599-0.0171-0.0696-0.03910.0520.02990.0314-0.0102-0.02390.01870.00810.0187-22.727517.3064-7.508
20.1039-0.25750.07631.22980.21650.35010.01030.02070.00460.017-0.0275-0.00290.02370.01430.01720.0156-0.00110.01280.0246-0.01260.017-23.6071-19.8956-21.6229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 268
2X-RAY DIFFRACTION1A3000
3X-RAY DIFFRACTION2B1 - 267
4X-RAY DIFFRACTION2B4000

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