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- PDB-7pwb: dTDP-sugar epimerase from Coxiella burnetii in complex with dTDP -

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Basic information

Entry
Database: PDB / ID: 7pwb
TitledTDP-sugar epimerase from Coxiella burnetii in complex with dTDP
ComponentsdTDP-4-dehydrorhamnose 3,5-epimerase
KeywordsSUGAR BINDING PROTEIN / Coxiella burnetii / O-antigen / epimerase / enzyme kinetics
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / : / cytosol
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
CITRIC ACID / THYMIDINE-5'-DIPHOSPHATE / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,40115
Polymers48,9742
Non-polymers2,42713
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-10 kcal/mol
Surface area16330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.882, 82.151, 163.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 2 - 187 / Label seq-ID: 24 - 209

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein dTDP-4-dehydrorhamnose 3,5-epimerase / Thymidine diphospho-4-keto-rhamnose 3 / 5-epimerase


Mass: 24486.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (strain RSA 493 / Nine Mile phase I) (bacteria)
Strain: RSA 493 / Nine Mile phase I / Gene: rfbC, CBU_1838 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q83AP3, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical
ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 7% PEG 4000 (w/v), 30% PEG 400, 5% dTDP (v/v), 29 mM citrate buffer pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.87→81.915 Å / Num. obs: 37452 / % possible obs: 84.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 12.5
Reflection shellResolution: 1.87→1.995 Å / Num. unique obs: 1874 / CC1/2: 0.67 / % possible all: 25

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
autoPROCdata scaling
autoPROCdata processing
Cootmodel building
STARANISOdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IXI

2ixi


Resolution: 1.87→81.915 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.709 / SU ML: 0.126 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.155
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2366 1856 4.956 %
Rwork0.209 35596 -
all0.21 --
obs-37452 84.439 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.645 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2--0.008 Å20 Å2
3----0.058 Å2
Refinement stepCycle: LAST / Resolution: 1.87→81.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 154 238 3512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133647
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173434
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.6514994
X-RAY DIFFRACTIONr_angle_other_deg1.2871.587961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6155443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03422.108204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79915643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2591525
X-RAY DIFFRACTIONr_chiral_restr0.0890.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024005
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02857
X-RAY DIFFRACTIONr_nbd_refined0.2030.2635
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.23063
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21523
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21671
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1110.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2650.219
X-RAY DIFFRACTIONr_nbd_other0.2880.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2180.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0510.21
X-RAY DIFFRACTIONr_mcbond_it3.5353.8561586
X-RAY DIFFRACTIONr_mcbond_other3.4983.8521584
X-RAY DIFFRACTIONr_mcangle_it4.7295.7611996
X-RAY DIFFRACTIONr_mcangle_other4.6965.761996
X-RAY DIFFRACTIONr_scbond_it4.24.5642059
X-RAY DIFFRACTIONr_scbond_other4.1994.5662060
X-RAY DIFFRACTIONr_scangle_it6.3836.722962
X-RAY DIFFRACTIONr_scangle_other6.3826.7212963
X-RAY DIFFRACTIONr_lrange_it8.62243.9583953
X-RAY DIFFRACTIONr_lrange_other8.6243.9753954
X-RAY DIFFRACTIONr_ncsr_local_group_10.0970.056226
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.097410.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.097410.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.87-1.9180.368110.3591780.35932280.5750.8095.8550.354
1.918-1.9710.378480.3429080.34431870.7190.82229.99690.344
1.971-2.0280.375980.33317910.33530730.7590.86461.47090.333
2.028-2.090.3061250.32124330.3229770.8450.88185.92540.312
2.09-2.1590.3671630.32227030.32428790.8380.88699.54850.307
2.159-2.2350.3351330.30626830.30728160.870.9021000.287
2.235-2.3190.3161360.27225760.27427120.8760.9171000.252
2.319-2.4130.3181390.26424650.26726040.8710.9261000.243
2.413-2.5210.2721180.24523890.24725080.910.93499.96010.224
2.521-2.6440.2671250.22322930.22524180.9190.9491000.208
2.644-2.7860.2591110.21721690.21922800.9240.9511000.202
2.786-2.9550.2351050.2120610.21121660.9280.9581000.201
2.955-3.1590.225880.2119880.21120770.9380.96199.95190.204
3.159-3.4120.272900.2117910.21218820.9210.96599.94690.212
3.412-3.7370.2011000.19416650.19517660.9550.96899.94340.199
3.737-4.1770.216690.16515290.16715990.9550.97499.93750.179
4.177-4.8210.146750.13413620.13514370.9820.9831000.158
4.821-5.8990.168640.16311430.16312100.9730.97899.75210.191
5.899-8.3210.256300.2019360.2039680.9330.96399.79340.231
8.321-81.9150.269280.2445330.2455670.9310.93298.94180.305

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