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- PDB-3m7w: Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) f... -

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Basic information

Entry
Database: PDB / ID: 3m7w
TitleCrystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 in Covalent Complex with Dehydroquinate
Components3-dehydroquinate dehydratase
KeywordsLYASE / Type I 3-Dehydroquinase / DHQase_I / Dehydroquinate / idp90922 / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / Schiff base / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
: / 3-dehydroquinate dehydratase, active site / Dehydroquinase class I active site. / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMinasov, G. / Light, S.H. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Insights into the mechanism of type I dehydroquinate dehydratases from structures of reaction intermediates.
Authors: Light, S.H. / Minasov, G. / Shuvalova, L. / Duban, M.E. / Caffrey, M. / Anderson, W.F. / Lavie, A.
History
DepositionMar 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
E: 3-dehydroquinate dehydratase
F: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,20826
Polymers165,7786
Non-polymers2,43020
Water19,9611108
1
A: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9167
Polymers55,2592
Non-polymers6575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-8 kcal/mol
Surface area19340 Å2
MethodPISA
2
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,19210
Polymers55,2592
Non-polymers9338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-14 kcal/mol
Surface area19420 Å2
MethodPISA
3
E: 3-dehydroquinate dehydratase
F: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1009
Polymers55,2592
Non-polymers8417
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-15 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.334, 66.576, 128.230
Angle α, β, γ (deg.)90.00, 119.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 27629.652 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: aroD, STM1358 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P58687, 3-dehydroquinate dehydratase
#2: Chemical
ChemComp-DQA / 1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID / 3-DEHYDROQUINIC ACID


Mass: 190.151 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H10O6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1108 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 295 K / pH: 4.6
Details: Protein solution: 7.5 mg/mL, 0.5M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen solution: ANL-2 (E7), 0.17M Ammonium acetate, 0.085M Sodium acetate (pH 4.6), 25.5% PEG 4000, 15% Glycerol; ...Details: Protein solution: 7.5 mg/mL, 0.5M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen solution: ANL-2 (E7), 0.17M Ammonium acetate, 0.085M Sodium acetate (pH 4.6), 25.5% PEG 4000, 15% Glycerol; Soak: 5mM Dehydroquinic acid in screen solution for 20 min., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2010 / Details: BERYLLIUM LENSES
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 99121 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L2I

3l2i


Resolution: 1.95→29.69 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.393 / SU ML: 0.098 / Isotropic thermal model: Refined individually / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 4942 5 %RANDOM
Rwork0.154 ---
obs0.157 94167 99.9 %-
all-94167 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å21.6 Å2
2---1.44 Å2-0 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11462 0 156 1108 12726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211968
X-RAY DIFFRACTIONr_bond_other_d0.0010.027930
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.97816221
X-RAY DIFFRACTIONr_angle_other_deg0.862319509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.05451540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90924.519478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.061152122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7191574
X-RAY DIFFRACTIONr_chiral_restr0.0840.21962
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213207
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022229
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_it1.1371.57604
X-RAY DIFFRACTIONr_mcbond_other0.3461.53104
X-RAY DIFFRACTIONr_mcangle_it1.936212311
X-RAY DIFFRACTIONr_scbond_it3.0734364
X-RAY DIFFRACTIONr_scangle_it4.9944.53910
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 370 -
Rwork0.201 6819 -
obs--99.08 %

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