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- PDB-4o9e: Crystal structure of QdtA, a sugar 3,4-ketoisemerase from Thermoa... -

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Basic information

Entry
Database: PDB / ID: 4o9e
TitleCrystal structure of QdtA, a sugar 3,4-ketoisemerase from Thermoanaerobacterium thermosaccharolyticum in complex with TDP
ComponentsQdtA
KeywordsISOMERASE / cupin / 3 / 4-ketoisomerase / TDP-sugar binding
Function / homology
Function and homology information


Sugar 3,4-ketoisomerase QdtA, cupin domain / WxcM-like, C-terminal / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-4TD / THYMINE / THYMIDINE-5'-DIPHOSPHATE / QdtA
Similarity search - Component
Biological speciesThermoanaerobacterium thermosaccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsThoden, J.B. / Holden, H.M.
CitationJournal: Protein Sci. / Year: 2014
Title: The molecular architecture of QdtA, a sugar 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum.
Authors: Thoden, J.B. / Holden, H.M.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: QdtA
B: QdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6316
Polymers34,3322
Non-polymers1,2994
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.788, 95.788, 94.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-202-

4TD

DetailsBiological dimer is composed of chains A+B

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Components

#1: Protein QdtA / 3 / 4-ketoisomerase


Mass: 17165.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium thermosaccharolyticum (bacteria)
Strain: E207-71 / Gene: qdtA / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q6TFC5
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-TDR / THYMINE


Mass: 126.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2O2
#4: Chemical ChemComp-4TD / (2S)-1-[3-[(2S)-2-oxidanylpropoxy]-2-[[(2S)-2-oxidanylpropoxy]methyl]-2-[[(2R)-2-oxidanylpropoxy]methyl]propoxy]propan-2-ol / tetraerythritol propoxylate


Mass: 368.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATE THE FOLLOWING: ALA 52-> SER, PHE 94 -> LEU, LEU 95 ->VAL, AND CYS 116 -> TYR WE ...AUTHOR STATE THE FOLLOWING: ALA 52-> SER, PHE 94 -> LEU, LEU 95 ->VAL, AND CYS 116 -> TYR WE BELIEVE ARE SEQUENCING ERRORS IN THE DATA BASE DEPOSITION AS PCR USING VARIOUS ENZYMES AND TECHNIQUES ALWAYS GAVE GENES WITH THIS SEQUENCE AND NOT THAT DEPOSITED, AND AS SUCH WE HAVE DISCUSSED THAT IN THE PAPER

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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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22-28% pentaerythritol propoxylate, 100 mM HEPPS, 10 mM TDP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 9, 2009 / Details: montel mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→38.83 Å / Num. all: 28352 / Num. obs: 28352 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 18.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2040 / Rsym value: 0.282 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.7.0029refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PA7

2pa7


Resolution: 2→38.83 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.939 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.148 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23946 1517 5.1 %RANDOM
Rwork0.19682 ---
all0.199 28352 --
obs0.19895 28352 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.695 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--0.68 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2→38.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 84 123 2490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192422
X-RAY DIFFRACTIONr_bond_other_d00.022341
X-RAY DIFFRACTIONr_angle_refined_deg2.392.0153278
X-RAY DIFFRACTIONr_angle_other_deg0.9635405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6035272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00623.818110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83315436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.91512
X-RAY DIFFRACTIONr_chiral_restr0.130.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02527
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 107 -
Rwork0.261 2040 -
obs--97.95 %

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