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- PDB-4o0q: Apo structure of a methyltransferase component involved in O-deme... -

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Basic information

Entry
Database: PDB / ID: 4o0q
TitleApo structure of a methyltransferase component involved in O-demethylation
ComponentsDihydropteroate synthase DHPS
KeywordsTRANSFERASE / TIM barrel / methyltransferase / THF/MTHF
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
Dihydropteroate synthase DHPS
Similarity search - Component
Biological speciesDesulfitobacterium hafniense DCB-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 14, 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 1.3Mar 20, 2024Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)63,5112
Polymers63,5112
Non-polymers00
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-37 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.670, 119.070, 58.150
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 DCB-2 (bacteria)
Strain: DCB-2 / DSM 10664 / Gene: Dhaf_0722 / Production host: Escherichia coli (E. coli) / References: UniProt: B8FW00
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Source detailsoverexpression in E. coli (DE3) BL21

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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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 277.15 K / pH: 7.5
Details: 100mM Tris pH 7.5, 100mM succinic acid, 15%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 23, 2013
RadiationMonochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.92→27.7 Å / Num. obs: 48906 / % possible obs: 100 %
Reflection shellResolution: 1.92→1.97 Å / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
BALBESphasing
REFMAC5.5.0102refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→27.69 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.948 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2463 5 %RANDOM
Rwork0.182 ---
obs0.184 46314 99.8 %-
all-48828 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2--0.05 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.92→27.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4111 0 0 413 4524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0224213
X-RAY DIFFRACTIONr_bond_other_d0.0010.022794
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.9815730
X-RAY DIFFRACTIONr_angle_other_deg1.08636898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0575547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35125.491173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83515740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0951523
X-RAY DIFFRACTIONr_chiral_restr0.1180.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02746
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_it1.2561.52730
X-RAY DIFFRACTIONr_mcbond_other0.3851.51092
X-RAY DIFFRACTIONr_mcangle_it2.24824407
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7631483
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.3194.51323
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: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 193 -
Rwork0.261 3313 -
obs--99.63 %

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