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- PDB-9ar1: Structure of Epimerase Mth373 bound to uridine-5'-diphosphate-xyl... -

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Basic information

Entry
Database: PDB / ID: 9ar1
TitleStructure of Epimerase Mth373 bound to uridine-5'-diphosphate-xylopyranose
ComponentsdTDP-glucose 4,6-dehydratase related protein
KeywordsSUGAR BINDING PROTEIN / Epimerase / pseudomurein / peptidoglycan / murein / GalE / WcaG / WbpP / WbmF / cell wall / Methanothermobacter
Function / homologyNAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / dTDP-glucose 4,6-dehydratase related protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsCarbone, V. / Schofield, L.R. / Sutherland-Smith, A.J. / Ronimus, R.S.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden Fund New Zealand
CitationJournal: To Be Published
Title: Structurally characterizing epimerases from the thermophilic pseudomurein-containing methanogen Methanothermobacter thermautotrophicus delta H
Authors: Carbone, V. / Schofield, L.R. / Sutherland-Smith, A.J. / Ronimus, R.S.
History
DepositionFeb 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 2.0Feb 19, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dTDP-glucose 4,6-dehydratase related protein
B: dTDP-glucose 4,6-dehydratase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,90912
Polymers83,2402
Non-polymers2,67010
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-39 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.327, 139.327, 226.946
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-722-

HOH

21A-780-

HOH

31A-781-

HOH

41B-657-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein dTDP-glucose 4,6-dehydratase related protein


Mass: 41619.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Gene: MTH_373 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O26473

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Non-polymers , 6 types, 483 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-UDX / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / UDP-ALPHA-D-XYLOPYRANOSE


Mass: 536.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N2O16P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate tribasic dihydrate, 18% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95368 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95368 Å / Relative weight: 1
ReflectionResolution: 1.96→44.75 Å / Num. obs: 59615 / % possible obs: 98.6 % / Redundancy: 19.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.037 / Rrim(I) all: 0.167 / Net I/σ(I): 16.3
Reflection shellResolution: 1.96→2.01 Å / % possible obs: 80.6 % / Redundancy: 17.6 % / Rmerge(I) obs: 0.615 / Num. measured all: 60087 / Num. unique obs: 3405 / CC1/2: 0.951 / Rpim(I) all: 0.145 / Rrim(I) all: 0.633 / Net I/σ(I) obs: 5.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→44.75 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.368 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20416 2945 5 %RANDOM
Rwork0.17064 ---
obs0.17233 56236 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.984 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20.66 Å20 Å2
2--1.32 Å20 Å2
3----4.29 Å2
Refinement stepCycle: 1 / Resolution: 1.97→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5143 0 173 474 5790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135526
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174967
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.6687495
X-RAY DIFFRACTIONr_angle_other_deg1.411.58611442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2575628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20521.39331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49315926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8891545
X-RAY DIFFRACTIONr_chiral_restr0.0860.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021356
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_it2.332.5492500
X-RAY DIFFRACTIONr_mcbond_other2.3272.5482499
X-RAY DIFFRACTIONr_mcangle_it3.2633.8073129
X-RAY DIFFRACTIONr_mcangle_other3.2633.8093130
X-RAY DIFFRACTIONr_scbond_it2.7472.8243026
X-RAY DIFFRACTIONr_scbond_other2.7472.8243027
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9194.1344366
X-RAY DIFFRACTIONr_long_range_B_refined5.40630.1556579
X-RAY DIFFRACTIONr_long_range_B_other5.40530.1536580
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10820 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.97→2.017 Å
RfactorNum. reflection% reflection
Rfree0.234 181 -
Rwork0.214 3560 -
obs--84.49 %

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