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- PDB-7pwh: Structure of the dTDP-sugar epimerase StrM -

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Basic information

Entry
Database: PDB / ID: 7pwh
TitleStructure of the dTDP-sugar epimerase StrM
ComponentsdTDP-4-keto-rhamnose 3,5-epimerase,dTDP-4-dehydrorhamnose 3,5-epimerase
KeywordsSUGAR BINDING PROTEIN / Coxiella burnetii / O-antigen / epimerase / enzyme kinetics
Function / homology
Function and homology information


streptomycin biosynthetic process / dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / carbohydrate metabolic process
Similarity search - Function
dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
THYMIDINE-5'-DIPHOSPHATE / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCross, A.R. / Harmer, N.J. / Isupov, M.N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M016404/1 United Kingdom
Defence Science and Technology Laboratory (DSTL)DSTLX-1000098217 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N001591/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases.
Authors: Cross, A.R. / Roy, S. / Vivoli Vega, M. / Rejzek, M. / Nepogodiev, S.A. / Cliff, M. / Salmon, D. / Isupov, M.N. / Field, R.A. / Prior, J.L. / Harmer, N.J.
History
DepositionOct 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 18, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: dTDP-4-keto-rhamnose 3,5-epimerase,dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8917
Polymers35,2061
Non-polymers6866
Water2,936163
1
AAA: dTDP-4-keto-rhamnose 3,5-epimerase,dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules

AAA: dTDP-4-keto-rhamnose 3,5-epimerase,dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,78314
Polymers70,4112
Non-polymers1,37212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5860 Å2
ΔGint-43 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.376, 131.542, 78.539
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11AAA-447-

HOH

21AAA-502-

HOH

31AAA-545-

HOH

41AAA-563-

HOH

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Components

#1: Protein dTDP-4-keto-rhamnose 3,5-epimerase,dTDP-4-dehydrorhamnose 3,5-epimerase / Thymidine diphospho-4-keto-rhamnose 3 / 5-epimerase / dTDP-4-keto-6-deoxyglucose 3 / dTDP-6-deoxy-D- ...Thymidine diphospho-4-keto-rhamnose 3 / 5-epimerase / dTDP-4-keto-6-deoxyglucose 3 / dTDP-6-deoxy-D-xylo-4-hexulose 3 / dTDP-L-rhamnose synthase


Mass: 35205.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: strM / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P29783, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 291 K / Method: microbatch
Details: 10% PEG 6000, 30% PEG 300, 100 mM CaCl2, 50 mM Tris pH 7.0 + 10 mM dTDP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.9→50.42 Å / Num. obs: 17624 / % possible obs: 99.4 % / Redundancy: 4.3 % / CC1/2: 0.991 / Net I/σ(I): 5.5
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 1122 / CC1/2: 0.312

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HMZ

4hmz


Resolution: 1.9→50.42 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.036 / SU ML: 0.158 / Cross valid method: FREE R-VALUE / ESU R: 0.174 / ESU R Free: 0.161 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2495 925 5.255 %
Rwork0.2009 16676 -
all0.203 --
obs-17601 99.138 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 28.068 Å2
Baniso -1Baniso -2Baniso -3
1--1.435 Å20 Å20 Å2
2--0.191 Å2-0 Å2
3---1.244 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 42 163 1772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121736
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.6532374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.32319.196112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79915274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8521525
X-RAY DIFFRACTIONr_chiral_restr0.1070.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021382
X-RAY DIFFRACTIONr_nbd_refined0.2090.2737
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21082
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2153
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.229
X-RAY DIFFRACTIONr_mcbond_it2.2722.468839
X-RAY DIFFRACTIONr_mcangle_it3.6363.6811054
X-RAY DIFFRACTIONr_scbond_it2.8782.898897
X-RAY DIFFRACTIONr_scangle_it4.454.1981306
X-RAY DIFFRACTIONr_lrange_it8.38247.1886974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.351770.3421204X-RAY DIFFRACTION99.4565
1.949-2.0030.333790.3131151X-RAY DIFFRACTION98.4
2.003-2.0610.249570.3021134X-RAY DIFFRACTION97.4632
2.061-2.1240.386470.2951158X-RAY DIFFRACTION99.6691
2.124-2.1940.307570.261081X-RAY DIFFRACTION99.8246
2.194-2.2710.243580.2381058X-RAY DIFFRACTION99.8211
2.271-2.3560.325530.2361045X-RAY DIFFRACTION99.909
2.356-2.4520.329590.23964X-RAY DIFFRACTION100
2.452-2.5610.291640.219946X-RAY DIFFRACTION99.8024
2.561-2.6860.233450.188908X-RAY DIFFRACTION99.7906
2.686-2.8310.229440.182872X-RAY DIFFRACTION99.7821
2.831-3.0020.262450.185830X-RAY DIFFRACTION99.8858
3.002-3.2090.291310.178772X-RAY DIFFRACTION99.8756
3.209-3.4660.224460.177723X-RAY DIFFRACTION99.0979
3.466-3.7950.174350.154645X-RAY DIFFRACTION96.4539
3.795-4.2420.222410.145590X-RAY DIFFRACTION97.3765
4.242-4.8950.15290.124542X-RAY DIFFRACTION99.3044
4.895-5.9860.204230.151470X-RAY DIFFRACTION98.7976
5.986-8.4310.225230.162363X-RAY DIFFRACTION98.2188
8.431-50.420.218120.233220X-RAY DIFFRACTION95.082

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