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- PDB-6smf: THE CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM ZYMOMONAS MOBILIS -

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Basic information

Entry
Database: PDB / ID: 6smf
TitleTHE CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM ZYMOMONAS MOBILIS
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
CITRATE ANION / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.343 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: Nanoscale Horiz. / Year: 2020
Title: Biomacromolecular charge chirality detected using chiral plasmonic nanostructures
Authors: Rodier, M. / Keijzer, C. / Milner, J. / Karimullah, A. / Roszak, A.W. / Barron, L.D. / Gadegaard, N. / Lapthorn, A.J. / Kadodwala, M.
#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
DepositionAug 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: 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 / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)65,79513
Polymers64,5104
Non-polymers1,2859
Water1,63991
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)197,38439
Polymers193,52912
Non-polymers3,85527
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area35590 Å2
ΔGint-172 kcal/mol
Surface area61420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.627, 133.627, 101.670
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
11D-202-

TRS

21D-202-

TRS

31D-203-

SO4

41D-203-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 146 / Label seq-ID: 6 - 149

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 16127.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: aroD, aroQ, ZMO0737, ZMO1_ZMO0737 / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5NPJ9, 3-dehydroquinate dehydratase

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Non-polymers , 5 types, 100 molecules

#2: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.37 % / Description: Triangular plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 15% PEG 8000, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 2.343→66.9 Å / Num. obs: 24281 / % possible obs: 94 % / Redundancy: 5.3 % / Biso Wilson estimate: 74.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.022 / Rrim(I) all: 0.05 / Net I/av σ(I): 18.4 / Net I/σ(I): 18.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.5 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.343-2.4811.1761.412150.5850.5561.30152.5
6.709-66.90.02157.9121210.010.023100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.59 Å66.81 Å
Translation4.59 Å66.81 Å

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Processing

Software
NameVersionClassification
XDSMar 15, 2019data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LWZ

3lwz


Resolution: 2.343→66.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 20.495 / SU ML: 0.212 / SU R Cruickshank DPI: 0.3938 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.394 / ESU R Free: 0.236 / SU Rfree Cruickshank DPI: 0.2358
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1226 5 %RANDOM
Rwork0.1643 ---
obs0.1667 23074 85.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 190.28 Å2 / Biso mean: 82.799 Å2 / Biso min: 33.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å2-0 Å2
2--0.26 Å2-0 Å2
3----0.84 Å2
Refinement stepCycle: final / Resolution: 2.343→66.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 84 91 4515
Biso mean--86.95 71.27 -
Num. residues----576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134507
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174207
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.6296150
X-RAY DIFFRACTIONr_angle_other_deg1.3451.5689719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4265576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77323.382204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00115704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1441519
X-RAY DIFFRACTIONr_chiral_restr0.0780.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025080
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02857
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A43210.06
12B43210.06
21A43470.07
22C43470.07
31A43320.07
32D43320.07
41B43520.06
42C43520.06
51B43120.06
52D43120.06
61C43670.06
62D43670.06
LS refinement shellResolution: 2.343→2.404 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 13 -
Rwork0.36 159 -
all-172 -
obs--8.17 %
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)
14.92971.18620.24172.8399-0.12564.45390.1974-0.3178-0.68130.2429-0.05430.87990.3605-0.5661-0.14310.0757-0.09020.03730.21640.14710.5938-27.8757-14.401514.7638
24.6944-0.8752-0.64424.26821.08682.89450.07470.8418-0.9394-0.80040.14540.59620.2507-0.1175-0.22010.4125-0.0582-0.30540.2836-0.24880.548-13.6414-23.5852-10.0988
35.17-0.15781.32235.8233-1.45991.9788-0.00840.73230.2767-0.76090.20651.08940.0196-0.4334-0.1980.28010.0054-0.34440.44510.17740.5065-27.36973.7943-9.7242
44.9971.8184-0.28262.50940.08934.48010.1833-0.9978-0.21770.9935-0.04570.64620.001-0.5879-0.13760.51830.04720.3370.53030.24790.3176-15.9965-7.296134.5772
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 301
2X-RAY DIFFRACTION2B3 - 301
3X-RAY DIFFRACTION3C3 - 201
4X-RAY DIFFRACTION4D3 - 301

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