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- PDB-8idu: Crystal structure of substrate bound-form dehydroquinate dehydrat... -

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Basic information

Entry
Database: PDB / ID: 8idu
TitleCrystal structure of substrate bound-form dehydroquinate dehydratase from Corynebacterium glutamicum
Components3-dehydroquinate dehydratase
KeywordsLYASE / Amino-acid biosynthesis
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, conserved site / Dehydroquinase class II signature. / Dehydroquinase, class II / Dehydroquinase, class II superfamily / Dehydroquinase class II
Similarity search - Domain/homology
1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLee, C.H. / Kim, S. / Kim, K.-J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Microbiol Biotechnol. / Year: 2023
Title: Structural and Biochemical Analysis of 3-Dehydroquinate Dehydratase from Corynebacterium glutamicum .
Authors: Lee, C.H. / Kim, S. / Seo, H. / Kim, K.J.
History
DepositionFeb 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,55630
Polymers98,7226
Non-polymers2,83424
Water15,187843
1
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
E: 3-dehydroquinate dehydratase
F: 3-dehydroquinate dehydratase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)203,11260
Polymers197,44312
Non-polymers5,66948
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area38660 Å2
ΔGint-353 kcal/mol
Surface area55710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.641, 165.275, 106.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11F-386-

HOH

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Components

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


Mass: 16453.623 Da / Num. of mol.: 6 / Mutation: R19A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: aroQ, aroD, Cgl0423, cg0503 / Plasmid: pET30
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O52377, 3-dehydroquinate dehydratase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DQA / 1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID / 3-DEHYDROQUINIC ACID


Mass: 190.151 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C7H10O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 843 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.55 Å3/Da / Density % sol: 65.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: Lithium sulfate, Ammonium sulfate, Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 83591 / % possible obs: 98.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.13 / Χ2: 0.062 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.034.20.32483861.906197.2
2.03-2.074.30.30384522.063197.5
2.07-2.114.30.27384262.075197.6
2.11-2.154.40.24684282.122197.6
2.15-2.24.40.22384412.294197.8
2.2-2.254.40.21284622.303197.9
2.25-2.314.40.19885062.247197.7
2.31-2.374.50.19484712.364198.4
2.37-2.444.50.18384842.427198.5
2.44-2.524.60.16685072.626198.3
2.52-2.614.70.15585792.756198.8
2.61-2.714.80.14685362.941198.8
2.71-2.844.90.13285693.221199.1
2.84-2.9950.12785454.02199
2.99-3.1750.11686174.809199.3
3.17-3.425.10.10286205.43199.4
3.42-3.765.10.09585856.781199.4
3.76-4.315.10.08785397.287198.9
4.31-5.4350.08186016.513199.6
5.43-504.80.08585816.922198.8

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Processing

Software
NameVersionClassification
REFMACv5.8.0267refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.25 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1692 4516 5.1 %RANDOM
Rwork0.14195 ---
obs0.14336 83591 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.103 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å2-0 Å2
2---0.22 Å20 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 2→30.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6389 0 177 843 7409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136815
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166482
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.6269261
X-RAY DIFFRACTIONr_angle_other_deg1.451.57214950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4875866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33223.922306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.608151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7641524
X-RAY DIFFRACTIONr_chiral_restr0.0850.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021328
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7531.4513494
X-RAY DIFFRACTIONr_mcbond_other1.7521.4493493
X-RAY DIFFRACTIONr_mcangle_it2.7392.1374350
X-RAY DIFFRACTIONr_mcangle_other2.7382.144351
X-RAY DIFFRACTIONr_scbond_it3.2171.9633321
X-RAY DIFFRACTIONr_scbond_other2.9961.9043286
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5792.6714858
X-RAY DIFFRACTIONr_long_range_B_refined7.56319.7547548
X-RAY DIFFRACTIONr_long_range_B_other7.20718.8847320
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.187 318 -
Rwork0.166 5943 -
obs--95.68 %

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