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

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Basic information

Entry
Database: PDB / ID: 6hsa
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


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-ETE / CITRATE ANION / SERINE / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesButyrivibrio crossotus DSM 2876 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.92 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 2.0Oct 30, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Item: _atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id ..._atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id / _pdbx_validate_close_contact.label_alt_id_1 / _pdbx_validate_symm_contact.label_alt_id_1
Revision 2.1Jan 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)17,1747
Polymers16,3881
Non-polymers7876
Water4,990277
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)51,52321
Polymers49,1633
Non-polymers2,36018
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area8800 Å2
ΔGint-150 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.476, 79.476, 72.033
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-203-

SO4

21A-203-

SO4

31A-204-

SO4

41A-204-

SO4

51A-351-

HOH

61A-371-

HOH

71A-503-

HOH

81A-558-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 283 molecules

#2: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#3: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.67 Å3/Da / Density % sol: 53.96 % / Description: hexagonal prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG 4000, 0.2M Ammonium sulfate, 0.1M sodium citrate pH 5.6

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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: 0.92→31.93 Å / Num. obs: 112975 / % possible obs: 96.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 6.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.03 / Rsym value: 0.055 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
0.923-0.9392.20.3312.650540.7620.2650.42685.9
2.504-31.9113.20.03829.653870.9960.0240.04592.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HS9

6hs9


Resolution: 0.92→31.93 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.29 / SU ML: 0.008 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.012 / ESU R Free: 0.014
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1198 5762 5.1 %RANDOM
Rwork0.1013 ---
obs0.1022 107213 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.07 Å2 / Biso mean: 12.663 Å2 / Biso min: 4.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å2-0 Å2
2---0.08 Å20 Å2
3---0.27 Å2
Refinement stepCycle: final / Resolution: 0.92→31.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 84 277 1511
Biso mean--16.81 31.53 -
Num. residues----145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121324
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181285
X-RAY DIFFRACTIONr_angle_refined_deg2.041.6671800
X-RAY DIFFRACTIONr_angle_other_deg0.7291.612939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1375171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46624.59574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55715243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.446155
X-RAY DIFFRACTIONr_chiral_restr0.1020.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021561
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02309
X-RAY DIFFRACTIONr_rigid_bond_restr3.71232609
X-RAY DIFFRACTIONr_sphericity_free28.0995133
X-RAY DIFFRACTIONr_sphericity_bonded9.32552722
LS refinement shellResolution: 0.923→0.947 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 420 -
Rwork0.196 7229 -
all-7649 -
obs--88.66 %
Refinement TLS params.Method: refined / Origin x: 26.078 Å / Origin y: -12.113 Å / Origin z: 12.96 Å
111213212223313233
T0.0147 Å20.0081 Å20.0004 Å2-0.0145 Å20.0032 Å2--0.0281 Å2
L0.7155 °20.0212 °2-0.0993 °2-0.4184 °2-0.057 °2--0.4156 °2
S0.0093 Å °0.0265 Å °0.0738 Å °0.0039 Å °0.0012 Å °0.0797 Å °-0.0405 Å °-0.0594 Å °-0.0105 Å °

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