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- PDB-6pnl: Structure of Epimerase Mth375 from the thermophilic pseudomurein-... -

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Basic information

Entry
Database: PDB / ID: 6pnl
TitleStructure of Epimerase Mth375 from the thermophilic pseudomurein-containing methanogen Methanothermobacter thermautotrophicus
ComponentsUDP-glucose 4-epimerase related protein
KeywordsISOMERASE / Pseudomurein / UDP-N-acetylglucosamine / epimerase / cell wall / Methanothermobacter
Function / homologyNAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE / UDP-glucose 4-epimerase related protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsCarbone, V. / Schofield, L.R. / Sutherland-Smith, A.J. / Ronimus, R.S.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New ZealandAGR1301 New Zealand
CitationJournal: To Be Published
Title: Structure of a UDP-GALE 4-epimerase (Mth375) from the thermophilic pseudomurein-containing methanogen Methanothermobacter thermautotrophicus
Authors: Carbone, V. / Schofield, L.R. / Sutherland-Smith, A.J. / Ronimus, R.S.
History
DepositionJul 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Source and taxonomy / Category: database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Dec 27, 2023Group: Structure summary / Category: entity / struct / Item: _entity.pdbx_ec / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucose 4-epimerase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3997
Polymers42,0491
Non-polymers1,3506
Water4,306239
1
A: UDP-glucose 4-epimerase related protein
hetero molecules

A: UDP-glucose 4-epimerase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,79814
Polymers84,0992
Non-polymers2,70012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area8170 Å2
ΔGint-59 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.311, 89.311, 174.695
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-676-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-glucose 4-epimerase related protein


Mass: 42049.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: O26475

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Non-polymers , 5 types, 245 molecules

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


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Sodium chloride, 1.6 M Ammonium sulfate 0.1 M Sodium HEPES, 3.0% w/v 1,8-Diaminooctane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953653 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953653 Å / Relative weight: 1
ReflectionResolution: 2.01→46.52 Å / Num. obs: 28060 / % possible obs: 99.7 % / Redundancy: 19.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.192 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.01-2.0718.70.9873661119580.8674.696.3
9-46.5213.90.07456114050.99527.599.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.351
Highest resolutionLowest resolution
Rotation46.52 Å2.13 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PMH

6pmh


Resolution: 2.01→46.52 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.015 / SU ML: 0.083 / SU R Cruickshank DPI: 0.1551 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.133
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 1379 4.9 %RANDOM
Rwork0.1619 ---
obs0.1633 26639 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.01 Å2 / Biso mean: 22.501 Å2 / Biso min: 10.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 2.01→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 86 240 3033
Biso mean--24.42 31.28 -
Num. residues----336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192944
X-RAY DIFFRACTIONr_bond_other_d0.0020.022710
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9864008
X-RAY DIFFRACTIONr_angle_other_deg0.95436225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43323.758149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73915470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7091523
X-RAY DIFFRACTIONr_chiral_restr0.0810.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
LS refinement shellResolution: 2.014→2.066 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 86 -
Rwork0.201 1902 -
all-1988 -
obs--97.79 %

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