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- PDB-4zu5: Crystal structure of the QdtA 3,4-Ketoisomerase from Thermoanaero... -

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Basic information

Entry
Database: PDB / ID: 4zu5
TitleCrystal structure of the QdtA 3,4-Ketoisomerase from Thermoanaerobacterium thermosaccharolyticum, apo form
ComponentsQdtA
KeywordsISOMERASE / cupin / 3 / 4-ketoisomerase
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-PXN / THYMIDINE / QdtA
Similarity search - Component
Biological speciesThermoanaerobacterium thermosaccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsThoden, J.B. / Vinogradov, E. / Gilbert, M. / Salinger, A.J. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2015
Title: Bacterial Sugar 3,4-Ketoisomerases: Structural Insight into Product Stereochemistry.
Authors: Thoden, J.B. / Vinogradov, E. / Gilbert, M. / Salinger, A.J. / Holden, H.M.
History
DepositionMay 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)35,1855
Polymers34,3322
Non-polymers8533
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.742, 93.742, 95.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein QdtA


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


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O5
#3: Chemical ChemComp-PXN / (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol / PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH)


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


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THE FOLLOWING: ALA 52-SER, PHE 94 - LEU, LEU 95 - VAL, AND CYS 116 - TYR, WE BELIEVE ...AUTHORS STATE THE FOLLOWING: ALA 52-SER, PHE 94 - LEU, LEU 95 - VAL, AND CYS 116 - TYR, WE BELIEVE ARE SEQUENCING ERRORS IN THE DATABASE DEPOSITION, AS PCR USING VARIOUS ENZYMES AND TECHNIQUES ALWAYS GAVE GENES WITH THIS SEQUENCE AND NOT THAT DEPOSITED

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 18-22% pentaerythrivol propoxylate (5/4), 100 mM Homo-pipes

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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: Jul 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 37504 / Num. obs: 37504 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 44.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 1.7 / % possible all: 87.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O9E

4o9e


Resolution: 1.8→38.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.073 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23662 1889 5 %RANDOM
Rwork0.20491 ---
obs0.20649 35613 93.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.345 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2--0.94 Å20 Å2
3----1.89 Å2
Refinement stepCycle: 1 / Resolution: 1.8→38.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 59 81 2417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192400
X-RAY DIFFRACTIONr_bond_other_d0.0010.022339
X-RAY DIFFRACTIONr_angle_refined_deg1.9342.0013244
X-RAY DIFFRACTIONr_angle_other_deg0.81835400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79223.694111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22215434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.851513
X-RAY DIFFRACTIONr_chiral_restr0.1240.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02531
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 123 -
Rwork0.306 2398 -
obs--86.78 %

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