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- PDB-3nnt: Crystal Structure of K170M Mutant of Type I 3-Dehydroquinate Dehy... -

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Basic information

Entry
Database: PDB / ID: 3nnt
TitleCrystal Structure of K170M Mutant of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 in Non-Covalent Complex with Dehydroquinate.
Components3-dehydroquinate dehydratase
KeywordsLYASE / Structural Genomics / 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: 1.6 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
DepositionJun 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 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 1.3Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5874
Polymers60,2072
Non-polymers3802
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-16 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.727, 43.548, 79.938
Angle α, β, γ (deg.)91.18, 101.27, 109.05
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 30103.324 Da / Num. of mol.: 2 / Mutation: K170M
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.: 2 / Source method: obtained synthetically / Formula: C7H10O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 1.96 Å3/Da / Density % sol: 37.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3
Details: Protein solution: 7.5 mG/mL, 0.25M Sodium chloride, 0.01M Tris pH 8.3, 2mM 3-Dehydroquinic acid (DHR); Screen solution: Classics F9, 0.05M Potassium phosphate, 20%(w/v) PEG 8000., VAPOR ...Details: Protein solution: 7.5 mG/mL, 0.25M Sodium chloride, 0.01M Tris pH 8.3, 2mM 3-Dehydroquinic acid (DHR); Screen solution: Classics F9, 0.05M Potassium phosphate, 20%(w/v) PEG 8000., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2010 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 58590 / Num. obs: 58590 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.25 / Num. unique all: 2852 / % possible all: 95

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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: 3LB0

3lb0


Resolution: 1.6→29.65 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.754 / SU ML: 0.061
Isotropic thermal model: Atomic thermal factors individually refined
Cross valid method: THROUGHOUT / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18749 2950 5.1 %RANDOM
Rwork0.1579 ---
all0.15942 55405 --
obs0.15942 55405 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.535 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.61 Å20.58 Å2
2--0.51 Å2-0.25 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3922 0 26 525 4473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224263
X-RAY DIFFRACTIONr_bond_other_d0.0010.022773
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9675824
X-RAY DIFFRACTIONr_angle_other_deg0.8536846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3625567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04624.593172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.68315760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2361524
X-RAY DIFFRACTIONr_chiral_restr0.080.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024856
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02820
X-RAY DIFFRACTIONr_mcbond_it0.961.52723
X-RAY DIFFRACTIONr_mcbond_other0.2711.51100
X-RAY DIFFRACTIONr_mcangle_it1.66724441
X-RAY DIFFRACTIONr_scbond_it2.69531540
X-RAY DIFFRACTIONr_scangle_it4.4984.51383
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 215 -
Rwork0.234 3978 -
obs-3978 95.17 %

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