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

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Basic information

Entry
Database: PDB / ID: 6hsr
TitleThe crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37, 40% ethanol as cryoprotectant
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
ETHANOL / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesPsychromonas ingrahamii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,35818
Polymers67,2134
Non-polymers1,14514
Water2,774154
1
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
hetero molecules

A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
hetero molecules

A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,07354
Polymers201,63812
Non-polymers3,43542
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area35510 Å2
ΔGint-460 kcal/mol
Surface area70580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.828, 138.828, 138.828
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11D-361-

HOH

21D-367-

HOH

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Components

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


Mass: 16803.170 Da / Num. of mol.: 4
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-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.32 Å3/Da / Density % sol: 62.92 % / Description: hexagonal prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% ME2K PEG, 0.1M Lithium sulphate, 0.1M HEPES pH 7.5. Cryoprotected with 40% ethanol vapour diffused into the crystallisation well.

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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 S 6M / Detector: PIXEL / Date: May 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2→69.51 Å / Num. obs: 56976 / % possible obs: 94.6 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.017 / Rrim(I) all: 0.057 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.05710.22.0331.328640.770.6762.14360.1
5.626-69.4149.40.04146.328520.9990.0130.04399.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.391 / Cor.coef. Fo:Fc: 0.716 / Cor.coef. Io to Ic: 0.742
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.2data scaling
AMoRE7.0.056phasing
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HSQ

6hsq


Resolution: 2→69.51 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 7.768 / SU ML: 0.101 / SU R Cruickshank DPI: 0.1353 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.121
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 2836 5 %RANDOM
Rwork0.1731 ---
obs0.1742 54128 94.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 188.47 Å2 / Biso mean: 86.399 Å2 / Biso min: 33.33 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2→69.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4672 0 62 154 4888
Biso mean--95.15 76.6 -
Num. residues----600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0134824
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174525
X-RAY DIFFRACTIONr_angle_refined_deg2.5281.6226543
X-RAY DIFFRACTIONr_angle_other_deg1.6851.5710474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8765602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91523.239247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82715824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4351524
X-RAY DIFFRACTIONr_chiral_restr0.1240.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.025379
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02951
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.518 133 -
Rwork0.516 2366 -
all-2499 -
obs--56.77 %
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)
13.04941.6160.56961.08-0.26382.2110.8143-1.27420.6150.6544-1.10650.4209-0.70261.03810.29220.8062-0.79860.19021.4564-0.19120.746125.85179.44991.344
21.9576-0.80620.291.91150.85431.6114-0.2096-0.00040.9504-0.24590.5424-1.3901-0.63460.7698-0.33270.4767-0.17480.01210.52-0.40711.313321.34794.06263.05
31.8798-0.1126-0.20350.2266-0.37613.65330.2629-0.1009-0.08120.2383-0.3621-0.0949-0.55322.71560.09920.5356-0.3901-0.13022.13190.16590.547934.24764.65964.327
42.2249-0.6322-0.31542.93840.44211.78420.1260.14250.6382-0.10290.1475-0.6723-0.59090.5952-0.27350.2819-0.18380.05620.3549-0.09550.36690.30795.02350.645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 149
2X-RAY DIFFRACTION2B-1 - 149
3X-RAY DIFFRACTION3C1 - 149
4X-RAY DIFFRACTION4D-2 - 149

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