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

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Basic information

Entry
Database: PDB / ID: 6hsq
TitleThe crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37 crystal form 1
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
3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesPsychromonas ingrahamii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 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. / 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)68,35016
Polymers67,2134
Non-polymers1,13712
Water10,395577
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)205,04948
Polymers201,63812
Non-polymers3,41136
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 area35090 Å2
ΔGint-422 kcal/mol
Surface area70520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.386, 139.386, 139.386
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-368-

HOH

21D-454-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 3.36 Å3/Da / Density % sol: 63.37 % / Description: pyramidal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1M Lithium Sulphate, 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: Mar 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.456→98.561 Å / Num. obs: 150335 / % possible obs: 95.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.028 / Rrim(I) all: 0.12 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1 / Redundancy: 9.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.456-1.4961.5467052575310.5360.5321.6361.562.6
4.063-98.5610.067094775180.9990.020.06335.8100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.42 / Cor.coef. Fo:Fc: 0.447 / Cor.coef. Io to Ic: 0.481
Highest resolutionLowest resolution
Rotation4 Å15 Å
Translation4 Å15 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
AMoRE7.0.052phasing
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RC9

4rc9


Resolution: 1.46→98.56 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.791 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0532 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.054
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1858 7523 5 %RANDOM
Rwork0.1682 ---
obs0.169 142816 95.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.11 Å2 / Biso mean: 25.658 Å2 / Biso min: 13.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.46→98.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4656 0 64 577 5297
Biso mean--35.65 36.15 -
Num. residues----600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0134886
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174558
X-RAY DIFFRACTIONr_angle_refined_deg2.1511.626647
X-RAY DIFFRACTIONr_angle_other_deg1.6251.57110574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.13123.307251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77515830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3921524
X-RAY DIFFRACTIONr_chiral_restr0.1250.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025495
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02970
LS refinement shellResolution: 1.456→1.494 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 353 -
Rwork0.276 6724 -
all-7077 -
obs--61.33 %
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)
10.5097-0.0582-0.40480.8343-0.12811.0225-0.0336-0.0917-0.01870.1758-0.0051-0.0891-0.03660.13730.03880.0518-0.0001-0.03760.06380.00540.041125.85179.44991.344
20.4248-0.01070.11020.5479-0.22420.4622-0.0102-0.00840.0316-0.01790.0092-0.0297-0.02480.00620.0010.0159-0.0165-0.00780.02430.00010.034321.34794.06263.05
30.2907-0.08160.07691.46020.10870.4666-0.0030.02190.0118-0.12010.0048-0.1810.04380.0947-0.00180.01910.0150.02240.04470.00790.052634.24764.65964.327
40.74460.2489-0.0770.5088-0.0620.28730.00950.05320.0313-0.0308-0.0032-0.0269-0.04040.0286-0.00620.0194-0.0117-0.00210.01830.01090.01090.30795.02350.645
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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