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- PDB-4zu7: X-ray structure if the QdtA 3,4-ketoisomerase from Thermoanaeroba... -

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Basic information

Entry
Database: PDB / ID: 4zu7
TitleX-ray structure if the QdtA 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum, double mutant Y17R/R97H, in complex with TDP
ComponentsQdtA
KeywordsISOMERASE / cupin isomerase 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-5'-DIPHOSPHATE / QdtA
Similarity search - Component
Biological speciesThermoanaerobacterium thermosaccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._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

Downloads & links

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Assembly

Deposited unit
A: QdtA
B: QdtA
C: QdtA
D: QdtA
E: QdtA
F: QdtA
G: QdtA
H: QdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,71217
Polymers137,1268
Non-polymers3,5869
Water3,225179
1
A: QdtA
B: QdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0864
Polymers34,2822
Non-polymers8042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-32 kcal/mol
Surface area12560 Å2
MethodPISA
2
C: QdtA
D: QdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4545
Polymers34,2822
Non-polymers1,1733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-32 kcal/mol
Surface area12820 Å2
MethodPISA
3
E: QdtA
F: QdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0864
Polymers34,2822
Non-polymers8042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-33 kcal/mol
Surface area12750 Å2
MethodPISA
4
G: QdtA
H: QdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0864
Polymers34,2822
Non-polymers8042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-33 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.557, 96.174, 111.755
Angle α, β, γ (deg.)90.00, 114.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
QdtA


Mass: 17140.793 Da / Num. of mol.: 8 / Mutation: Y17R, R97H
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): Rosettsa2(DE3) / References: UniProt: Q6TFC5
#2: Chemical
ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#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.: 179 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THESE CONFLICTS MIGHT BE DUE TO STRAIN VARIANCE OR ERRORS IN THE INITIAL ...AUTHORS STATE THAT THESE CONFLICTS MIGHT BE DUE TO STRAIN VARIANCE OR ERRORS IN THE INITIAL SEQUENCING OF GENE THAT WAS DEPOSITED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20-24% pentaerythrivol propoxylate (pp 5/4), 100 mM MES

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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: Apr 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 52869 / Num. obs: 52869 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 10.1
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 1.8 / % possible all: 79.3

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Processing

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

4o9e


Resolution: 2.3→29.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.311 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.416 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25624 2660 5 %RANDOM
Rwork0.19239 ---
obs0.19564 50208 90.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.576 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-1.18 Å2
2--1.92 Å20 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 2.3→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9126 0 225 179 9530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199601
X-RAY DIFFRACTIONr_bond_other_d0.0010.029282
X-RAY DIFFRACTIONr_angle_refined_deg1.7762.00113005
X-RAY DIFFRACTIONr_angle_other_deg0.802321438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3551095
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22123.829444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.489151750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2881548
X-RAY DIFFRACTIONr_chiral_restr0.0960.21422
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022118
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 183 -
Rwork0.248 3242 -
obs--79.1 %

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