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- PDB-2x0f: Structure of WsaF in complex with dTDP-beta-L-Rha -

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Basic information

Entry
Database: PDB / ID: 2x0f
TitleStructure of WsaF in complex with dTDP-beta-L-Rha
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
2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / WsaF
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 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 1.3Dec 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)97,9278
Polymers96,4622
Non-polymers1,4656
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-28.4 kcal/mol
Surface area30900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.940, 75.650, 77.480
Angle α, β, γ (deg.)90.00, 102.78, 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 388:398 OR RESSEQ 402:413 )
211CHAIN B AND (RESSEQ 28:381 OR RESSEQ 388:398 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N2O15P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.16 Å3/Da / Density % sol: 42.98 % / Description: NONE
Crystal growDetails: 0.2 MM MG FORMATE, 20% PEG3350

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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: 2.55→28.8 Å / Num. obs: 52047 / % possible obs: 94.8 % / Observed criterion σ(I): 2.55 / Redundancy: 1.9 % / Biso Wilson estimate: 54.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.5 / % possible all: 66.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_216)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X0D

2x0d


Resolution: 2.55→28.43 Å / SU ML: 0.35 / σ(F): 0.96 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 2603 5 %
Rwork0.186 --
obs0.188 52027 94.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.6 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.8865 Å2-0 Å2-3.1346 Å2
2--7.0298 Å2-0 Å2
3----4.1434 Å2
Refinement stepCycle: LAST / Resolution: 2.55→28.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6239 0 94 215 6548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0266492
X-RAY DIFFRACTIONf_angle_d1.3568791
X-RAY DIFFRACTIONf_dihedral_angle_d19.6872463
X-RAY DIFFRACTIONf_chiral_restr0.26946
X-RAY DIFFRACTIONf_plane_restr0.0021106
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3096X-RAY DIFFRACTIONPOSITIONAL
12B3096X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5503-2.64140.32592060.26293719X-RAY DIFFRACTION71
2.6414-2.74710.30932260.24524837X-RAY DIFFRACTION93
2.7471-2.8720.28782540.23075093X-RAY DIFFRACTION98
2.872-3.02320.27163120.21865103X-RAY DIFFRACTION98
3.0232-3.21240.26922580.21825073X-RAY DIFFRACTION98
3.2124-3.460.25012890.19255157X-RAY DIFFRACTION99
3.46-3.80750.20942610.17165144X-RAY DIFFRACTION99
3.8075-4.35680.17022550.14125172X-RAY DIFFRACTION99
4.3568-5.48260.18172870.13415117X-RAY DIFFRACTION99
5.4826-28.43140.18142550.16595009X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -16.439 Å / Origin y: 4.9208 Å / Origin z: -6.136 Å
111213212223313233
T0.0091 Å20.0013 Å20.0233 Å2-0.0182 Å20.0086 Å2--0.0603 Å2
L0.8448 °20.0777 °2-0.2622 °2-0.2761 °20.012 °2--0.7709 °2
S-0.0072 Å °0.1719 Å °-0.0841 Å °-0.0409 Å °0.0135 Å °0.0158 Å °-0.0349 Å °-0.0682 Å °-0.0082 Å °
Refinement TLS groupSelection details: CHAIN A

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