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- PDB-2x0e: Complex structure of WsaF with dTDP -

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Basic information

Entry
Database: PDB / ID: 2x0e
TitleComplex structure of WsaF with dTDP
ComponentsWSAF
KeywordsTRANSFERASE / GT4 FAMILY
Function / homology
Function and homology information


polysaccharide binding
Similarity search - Function
Rossmann fold - #11090 / : / WsaF, N-terminal domain / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-DIPHOSPHATE / WsaF
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsSteiner, K. / Hagelueken, G. / Naismith, J.H.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Basis of Substrate Binding in Wsaf, a Rhamnosyltransferase from Geobacillus Stearothermophilus.
Authors: Steiner, K. / Hagelueken, G. / Messner, P. / Schaeffer, C. / Naismith, J.H.
History
DepositionDec 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WSAF
B: WSAF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5437
Polymers96,4622
Non-polymers1,0815
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-34.18 kcal/mol
Surface area30830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.820, 75.560, 77.710
Angle α, β, γ (deg.)90.00, 103.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 28:381 OR RESSEQ 389:398 OR RESSEQ 402:413 )
211CHAIN B AND (RESSEQ 28:381 OR RESSEQ 389:398 OR RESSEQ 402:413 )

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Components

#1: Protein WSAF / RHAMNOSYLTRANSFERASE


Mass: 48231.059 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Strain: 2004/3A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7BG50
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 78 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 79 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, LYS 78 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 79 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 81 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 78 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 79 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 81 TO ALA

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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: 2.17 Å3/Da / Density % sol: 43.4 % / Description: NONE
Crystal growTemperature: 293 K / Details: 0.2 MM MG FORMATE, 20% PEG3350, 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU-MSC SATURN 944 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.81→29.6 Å / Num. obs: 38750 / % possible obs: 95.1 % / Observed criterion σ(I): 2.55 / Redundancy: 1.9 % / Biso Wilson estimate: 32.89 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.6
Reflection shellResolution: 2.81→2.91 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.55 / % possible all: 68.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X0D

2x0d


Resolution: 2.81→29.63 Å / SU ML: 0.45 / σ(F): 0.96 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 1971 5.1 %
Rwork0.185 --
obs0.188 38728 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.43 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1--8.0703 Å20 Å2-3.0078 Å2
2--9.0152 Å2-0 Å2
3----0.9449 Å2
Refinement stepCycle: LAST / Resolution: 2.81→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6193 0 68 114 6375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046417
X-RAY DIFFRACTIONf_angle_d0.8098688
X-RAY DIFFRACTIONf_dihedral_angle_d16.7642356
X-RAY DIFFRACTIONf_chiral_restr0.057935
X-RAY DIFFRACTIONf_plane_restr0.0021097
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3087X-RAY DIFFRACTIONPOSITIONAL
12B3087X-RAY DIFFRACTIONPOSITIONAL0.037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8142-2.91470.33081380.26262758X-RAY DIFFRACTION72
2.9147-3.03130.33681600.25293597X-RAY DIFFRACTION92
3.0313-3.16910.29712290.22773758X-RAY DIFFRACTION99
3.1691-3.3360.22841950.20523827X-RAY DIFFRACTION99
3.336-3.54470.27542240.18923836X-RAY DIFFRACTION99
3.5447-3.81790.23062150.16943825X-RAY DIFFRACTION99
3.8179-4.20110.22312170.15153799X-RAY DIFFRACTION99
4.2011-4.80680.19691880.13793822X-RAY DIFFRACTION99
4.8068-6.04760.21052100.14433817X-RAY DIFFRACTION99
6.0476-29.62990.21821950.16493718X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.557-0.1232-0.08590.4185-0.0430.8520.00670.1674-0.0433-0.0199-0.02160.019-0.0243-0.07990.02080.022-0.01120.01060.06760.00920.0196-16.44944.8972-6.1706
21.40410.16520.19650.2117-0.23910.39420.0287-0.4262-0.04310.0754-0.0299-0.0232-0.04180.01520.00880.06780.0318-0.01410.1353-0.02210.0109-13.96666.903628.3661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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