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- PDB-6hsu: The crystal structure of type II Dehydroquinase from Psychromonas... -

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Basic information

Entry
Database: PDB / ID: 6hsu
TitleThe crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37, crystal form 2
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
L(+)-TARTARIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesPsychromonas ingrahamii (bacteria)
Psychromonas ingrahamii 37 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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 Psychromonas ingrahamii 37
Authors: Lapthorn, A.J. / Koyroytsaltis-McQuire, D. / 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
DepositionOct 1, 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

Downloads & links

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
E: 3-dehydroquinate dehydratase
F: 3-dehydroquinate dehydratase
G: 3-dehydroquinate dehydratase
H: 3-dehydroquinate dehydratase
I: 3-dehydroquinate dehydratase
J: 3-dehydroquinate dehydratase
K: 3-dehydroquinate dehydratase
L: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,74026
Polymers201,63812
Non-polymers2,10214
Water25,4371412
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32260 Å2
ΔGint-86 kcal/mol
Surface area70340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.572, 137.948, 139.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 16803.170 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychromonas ingrahamii (strain 37) (bacteria)
Strain: 37 / Gene: aroQ, Ping_3121 / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1SZA3, 3-dehydroquinate dehydratase
#2: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C4H6O6 / Source: (gene. exp.) Psychromonas ingrahamii 37 (bacteria) / Gene: aroQ / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: 3-dehydroquinate dehydratase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1412 / 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: 3.28 Å3/Da / Density % sol: 62.5 % / Description: hexagonal prism
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M sodium chloride, 0.2M sodium tartrate, 0.1M MOPS pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.6→137.57 Å / Num. obs: 346154 / % possible obs: 99.7 % / Redundancy: 5.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.052 / Rrim(I) all: 0.12 / Net I/σ(I): 7.3 / Num. measured all: 1904219 / Scaling rejects: 4960
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.635.73.327168290.1681.5633.68898.4
8.76-137.575.50.0622930.9910.0280.06698.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.33 / Cor.coef. Fo:Fc: 0.729 / Cor.coef. Io to Ic: 0.7
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Aimless0.6.2data scaling
AMoRE7.0.052phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HSQ

6hsq


Resolution: 1.6→79.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2061 / WRfactor Rwork: 0.1881 / FOM work R set: 0.808 / SU B: 3.829 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0758 / SU Rfree: 0.0741 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 17403 5 %RANDOM
Rwork0.1911 ---
obs0.1919 328295 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.57 Å2 / Biso mean: 33.889 Å2 / Biso min: 17.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å20 Å2
2--0.34 Å20 Å2
3----1.29 Å2
Refinement stepCycle: final / Resolution: 1.6→79.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13969 0 139 1412 15520
Biso mean--47.27 41.49 -
Num. residues----1802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01314607
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713725
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.63219865
X-RAY DIFFRACTIONr_angle_other_deg1.5291.57331873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55251886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41223.27737
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87152526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0731572
X-RAY DIFFRACTIONr_chiral_restr0.1010.22002
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022874
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 1099 -
Rwork0.315 24391 -
all-25490 -
obs--99.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8407-1.1497-0.31941.11330.09510.8159-0.0915-0.0256-0.40750.07330.02640.25520.1158-0.19240.0650.0704-0.04790.02690.0620.01230.281946.66643.07579.653
20.4370.14160.07610.7817-0.59021.2857-0.0185-0.0406-0.03950.0115-0.0273-0.08320.04650.12060.04580.0070.0105-0.00880.03760.01680.183587.7468.30793.956
30.40030.03250.12610.87980.20970.488-0.0065-0.00030.04970.0159-0.03080.0313-0.0268-0.05640.03730.01070.0242-0.00030.062-0.00190.19147.05993.10477.233
40.70940.2723-0.25340.6623-0.18640.8477-0.0225-0.02180.00530.03790.00580.02540.0994-0.10680.01670.0237-0.02990.01860.0762-0.00330.17533.82463.71276.404
50.6069-0.00380.02171.4129-0.34570.86280.04330.0319-0.1576-0.1338-0.0213-0.06180.09540.0097-0.0220.02080.0069-0.01070.0229-0.03650.210876.46347.70642.915
61.13150.1032-0.36510.3635-0.03190.98490.02830.01240.0985-0.0107-0.0062-0.0311-0.09370.0681-0.02210.0129-0.01420.01280.0256-0.00110.187593.18487.68868.511
70.73910.15670.33540.5069-0.05270.78730.0494-0.0444-0.10620.0095-0.0006-0.02990.0979-0.0098-0.04880.0635-0.00640.00330.00540.02230.18475.24947.27993.613
80.49110.17-0.06821.12280.65911.6203-0.00750.0889-0.08950.21110.0556-0.10140.310.0986-0.04810.09460.0278-0.02580.0285-0.02970.238572.89434.76663.578
90.7473-0.0796-0.4960.5136-0.08571.5532-0.00340.1123-0.0355-0.07510.00930.0221-0.0461-0.2601-0.00590.01580.0028-0.00690.1019-0.00590.165141.178.97848.678
101.1904-0.47320.10530.9219-0.03520.4199-0.0492-0.07290.07990.11040.0517-0.0128-0.0496-0.0464-0.00250.02440.0221-0.00170.0326-0.01460.160968.55393.63288.824
110.9210.2465-0.03150.73720.15630.6314-0.03370.0675-0.0198-0.04490.0369-0.03650.00010.0478-0.00310.0043-0.00550.01480.0533-0.01240.154391.63675.76947.36
121.2596-0.15650.27870.46-0.09010.44060.00340.10510.021-0.0241-0.02050.0522-0.01680.03150.01710.0031-0.005-0.00740.0566-0.00790.152561.52374.86535.676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 149
2X-RAY DIFFRACTION2B0 - 149
3X-RAY DIFFRACTION3C0 - 149
4X-RAY DIFFRACTION4D-2 - 149
5X-RAY DIFFRACTION5E2 - 149
6X-RAY DIFFRACTION6F-1 - 149
7X-RAY DIFFRACTION7G-2 - 149
8X-RAY DIFFRACTION8H0 - 149
9X-RAY DIFFRACTION9I0 - 149
10X-RAY DIFFRACTION10J-1 - 149
11X-RAY DIFFRACTION11K-1 - 149
12X-RAY DIFFRACTION12L1 - 149

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