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- PDB-8idr: Crystal structure of apo-form of dehydroquinate dehydratase from ... -

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Basic information

Entry
Database: PDB / ID: 8idr
TitleCrystal structure of apo-form of dehydroquinate dehydratase from Corynebacterium glutamicum
Components3-dehydroquinate dehydratase
KeywordsLYASE / Aromatic 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
CITRATE ANION / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

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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)67,1109
Polymers66,1594
Non-polymers9515
Water10,611589
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)201,32927
Polymers198,47712
Non-polymers2,85215
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area31640 Å2
ΔGint-53 kcal/mol
Surface area60340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.531, 81.531, 221.807
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-377-

HOH

21B-480-

HOH

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Components

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


Mass: 16539.738 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: aroQ, aroD, Cgl0423, cg0503
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O52377, 3-dehydroquinate dehydratase
#2: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, Ammonium citrate tribasic

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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 4, 2022
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 47482 / % possible obs: 99 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.065 / Χ2: 0.043 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.832.70.27451382.041199
1.83-1.862.70.25850742.165199.1
1.86-1.92.70.2150412.261199.1
1.9-1.942.70.1950662.383199.3
1.94-1.982.70.16450342.471199.2
1.98-2.032.70.14250052.688199.4
2.03-2.082.70.12251072.833199.4
2.08-2.132.70.11250793.034199.4
2.13-2.22.80.09650793.156199.4
2.2-2.272.80.09250243.1199.5
2.27-2.352.80.08451053.074199.4
2.35-2.442.80.07750513.145199.5
2.44-2.552.80.07150613.21199.5
2.55-2.692.80.06250823.168199.6
2.69-2.862.80.05750523.28199.4
2.86-3.082.80.05150833.253199.6
3.08-3.392.80.04750833.417199.7
3.39-3.882.70.04250823.364199.1
3.88-4.882.50.04149803.402198
4.88-502.50.04447414.108192.8

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Processing

Software
NameVersionClassification
REFMACv5.8.0267refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→26.51 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.577 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20279 2494 5 %RANDOM
Rwork0.15778 ---
obs0.16006 47482 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.309 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å2-0 Å2
3----1.29 Å2
Refinement stepCycle: 1 / Resolution: 1.8→26.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4369 0 65 589 5023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134517
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154317
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.6236132
X-RAY DIFFRACTIONr_angle_other_deg1.4471.5729944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5915578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70523.349212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97915727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0711520
X-RAY DIFFRACTIONr_chiral_restr0.080.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025136
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02908
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_it1.9772.3172327
X-RAY DIFFRACTIONr_mcbond_other1.9592.3152326
X-RAY DIFFRACTIONr_mcangle_it2.8133.4512900
X-RAY DIFFRACTIONr_mcangle_other2.8173.4552901
X-RAY DIFFRACTIONr_scbond_it2.9392.7012190
X-RAY DIFFRACTIONr_scbond_other2.9362.7012189
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2493.9083233
X-RAY DIFFRACTIONr_long_range_B_refined6.01829.875045
X-RAY DIFFRACTIONr_long_range_B_other5.88529.2554905
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 245 -
Rwork0.207 3490 -
obs--98.24 %

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