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- PDB-6hs8: The crystal structure of type II Dehydroquinase from Butyrivibrio... -

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Basic information

Entry
Database: PDB / ID: 6hs8
TitleThe crystal structure of type II Dehydroquinase from Butyrivibrio crossotus DSM 2876
Components3-dehydroquinate dehydratase
KeywordsBIOSYNTHETIC PROTEIN / shikimate pathway / dehydratase
Function / homology
Function and homology information


quinate catabolic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Dehydroquinase, class II / Dehydroquinase, class II, conserved site / Dehydroquinase class II signature. / Dehydroquinase, class II / Dehydroquinase, class II superfamily / Dehydroquinase class II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / L(+)-TARTARIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesButyrivibrio crossotus DSM 2876 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsLapthorn, A.J. / Roszak, A.W.
Citation
Journal: To Be Published
Title: The crystal structure of type II Dehydroquinase from Butyrivibrio crossotus DSM 2876
Authors: Lapthorn, A.J. / Robertson, H. / Roszak, A.W.
#1: Journal: AMB Express / Year: 2015
Title: Unraveling the kinetic diversity of microbial 3-dehydroquinate dehydratases of shikimate pathway.
Authors: Liu, C. / Liu, Y.M. / Sun, Q.L. / Jiang, C.Y. / Liu, S.J.
#2: Journal: Structure / Year: 2002
Title: The structure and mechanism of the type II dehydroquinase from Streptomyces coelicolor.
Authors: Roszak, A.W. / Robinson, D.A. / Krell, T. / Hunter, I.S. / Fredrickson, M. / Abell, C. / Coggins, J.R. / Lapthorn, A.J.
History
DepositionSep 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9686
Polymers16,3301
Non-polymers6375
Water2,414134
1
A: 3-dehydroquinate dehydratase
hetero molecules

A: 3-dehydroquinate dehydratase
hetero molecules

A: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,90318
Polymers48,9913
Non-polymers1,91215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area9070 Å2
ΔGint-34 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.330, 125.330, 125.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-204-

PO4

21A-204-

PO4

31A-319-

HOH

41A-337-

HOH

51A-355-

HOH

61A-418-

HOH

71A-434-

HOH

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Components

#1: Protein 3-dehydroquinate dehydratase / 3-dehydroquinase / Type II DHQase


Mass: 16330.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Butyrivibrio crossotus DSM 2876 (bacteria)
Gene: aroQ, BUTYVIB_01550 / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D4S0D1, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.02 % / Description: pyramidal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 10% MPD, 0.1M Sodium tartrate, 0.1M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.7→37.79 Å / Num. obs: 17966 / % possible obs: 99.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 27.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.025 / Rrim(I) all: 0.06 / Net I/av σ(I): 17.4 / Net I/σ(I): 18.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.518 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 888 / CC1/2: 0.554 / Rpim(I) all: 0.702 / Rrim(I) all: 1.677 / % possible all: 99.89

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.38 Å37.79 Å
Translation4.38 Å37.79 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GQO

1gqo


Resolution: 1.7→37.79 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.01 / SU ML: 0.063 / SU R Cruickshank DPI: 0.0831 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.087
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1793 854 4.8 %RANDOM
Rwork0.1416 ---
obs0.1433 17098 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.67 Å2 / Biso mean: 31.16 Å2 / Biso min: 19.75 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.7→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 41 134 1320
Biso mean--45.61 44.05 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0141233
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171077
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.6821671
X-RAY DIFFRACTIONr_angle_other_deg1.0081.652534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26424.69766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03415217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.98154
X-RAY DIFFRACTIONr_chiral_restr0.1010.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
LS refinement shellResolution: 1.7→1.745 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 66 -
Rwork0.269 1236 -
all-1302 -
obs--99.85 %

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