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

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Basic information

Entry
Database: PDB / ID: 6pmh
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 / nucleotide binding / ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / 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: 2.3 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 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 27, 2023Group: Database references / Structure summary / Category: pdbx_database_related / struct / Item: _struct.title
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)43,0758
Polymers41,9731
Non-polymers1,1017
Water4,720262
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)86,14916
Polymers83,9462
Non-polymers2,20314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_557-x+2/3,-x+y+1/3,-z+7/31
Buried area8090 Å2
ΔGint-89 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.815, 113.815, 239.873
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-639-

HOH

21A-681-

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: 41973.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (archaea)
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H
Gene: MTH_375 / Production host: Escherichia coli (E. coli) / References: UniProt: O26475

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Non-polymers , 6 types, 269 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.57 Å3/Da / Density % sol: 65.54 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.0 M ammonium dihydrogen phosphate, 0.1 M tri-sodium citrate, Silver Bullets Bio condition H9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9117 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9117 Å / Relative weight: 1
ReflectionResolution: 2.3→48.27 Å / Num. obs: 26918 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.176 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.3-2.3811.30.7632954826070.9053.7100
8.91-48.279.40.04149165210.99946.499.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å48.27 Å
Translation2.2 Å48.27 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.27data scaling
PHASER2.6.1phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PZJ

2pzj


Resolution: 2.3→48.27 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.097 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1646 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.144
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1776 1380 5.1 %RANDOM
Rwork0.1471 ---
obs0.1487 25527 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 99.69 Å2 / Biso mean: 25.768 Å2 / Biso min: 9.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.4 Å2-0 Å2
2--0.79 Å2-0 Å2
3----2.58 Å2
Refinement stepCycle: final / Resolution: 2.3→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 67 263 2982
Biso mean--24.49 31.45 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192849
X-RAY DIFFRACTIONr_bond_other_d0.0020.022626
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9753877
X-RAY DIFFRACTIONr_angle_other_deg0.98636031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08123.81147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33515460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.771523
X-RAY DIFFRACTIONr_chiral_restr0.0950.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213253
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02695
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 106 -
Rwork0.188 1866 -
all-1972 -
obs--99.95 %

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