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- PDB-6hs9: The crystal structure of type II Dehydroquinase from Butyrivibrio... -

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Basic information

Entry
Database: PDB / ID: 6hs9
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
Chem-3DS / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesButyrivibrio crossotus DSM 2876 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.05 Å
AuthorsLapthorn, A.J. / Roszak, A.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/P00086X/1 United Kingdom
Citation
Journal: To Be Published
Title: The crystal structure of type II Dehydroquinase from Butyrivibrio crossotus DSM 2876
Authors: Lapthorn, A.J. / Ner, L. / 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)16,5602
Polymers16,3881
Non-polymers1721
Water4,576254
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)49,6796
Polymers49,1633
Non-polymers5163
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area4410 Å2
ΔGint-11 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.550, 79.550, 72.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-348-

HOH

21A-352-

HOH

31A-391-

HOH

41A-512-

HOH

51A-529-

HOH

61A-554-

HOH

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Components

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


Mass: 16387.510 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-3DS / (4S,5R)-4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylic acid / 3-dehydroshikimate


Mass: 172.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.69 Å3/Da / Density % sol: 54.2 % / Description: hexagonal prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% PEG 8000, 0.1M CaCl2, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.82656 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 1.05→32.04 Å / Num. obs: 119959 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 12.298 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.028 / Rrim(I) all: 0.047 / Net I/σ(I): 13.9 / Num. measured all: 292996
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2186 / CC1/2: 0.477 / Rpim(I) all: 0.559 / Rrim(I) all: 0.914 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.05 Å32 Å
Translation1.05 Å32 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.29data scaling
PHASER2.5.6phasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GQO

1gqo


Resolution: 1.05→32 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.72 / SU ML: 0.015 / SU R Cruickshank DPI: 0.0186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.019 / ESU R Free: 0.02
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.134 4062 5.1 %RANDOM
Rwork0.1128 ---
obs0.1139 74983 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74 Å2 / Biso mean: 21.112 Å2 / Biso min: 8.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.1 Å2-0 Å2
2---0.21 Å20 Å2
3---0.68 Å2
Refinement stepCycle: final / Resolution: 1.05→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 19 254 1423
Biso mean--20.81 40.15 -
Num. residues----145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0121246
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181209
X-RAY DIFFRACTIONr_angle_refined_deg2.0511.641694
X-RAY DIFFRACTIONr_angle_other_deg0.7121.5812757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99824.85368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48815228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.117154
X-RAY DIFFRACTIONr_chiral_restr0.1290.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021491
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02298
X-RAY DIFFRACTIONr_rigid_bond_restr5.07632455
X-RAY DIFFRACTIONr_sphericity_free24.668585
X-RAY DIFFRACTIONr_sphericity_bonded12.95652492
LS refinement shellResolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 301 -
Rwork0.338 5571 -
all-5872 -
obs--99.14 %

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