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- PDB-4l8l: Crystal Structure of the Type II Dehydroquinase from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 4l8l
TitleCrystal Structure of the Type II Dehydroquinase from Pseudomonas aeruginosa
Components3-dehydroquinate dehydratase 1
KeywordsLYASE / Flavodoxin-like fold / Rossmann Fold / alpha helix / beta sheet / Dehydratase / Dehydroquinic acid
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
3-dehydroquinate dehydratase 1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsReiling, S.A. / Asojo, O.A.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structure of type II dehydroquinase from Pseudomonas aeruginosa.
Authors: Reiling, S. / Kelleher, A. / Matsumoto, M.M. / Robinson, G. / Asojo, O.A.
History
DepositionJun 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase 1


Theoretical massNumber of molelcules
Total (without water)15,9851
Polymers15,9851
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 3-dehydroquinate dehydratase 1

A: 3-dehydroquinate dehydratase 1


Theoretical massNumber of molelcules
Total (without water)31,9702
Polymers31,9702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y+1/2,-z+1/21
Buried area1840 Å2
ΔGint-6 kcal/mol
Surface area12860 Å2
MethodPISA
3
A: 3-dehydroquinate dehydratase 1
x 12


Theoretical massNumber of molelcules
Total (without water)191,82012
Polymers191,82012
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_645z+1,x-1,y1
crystal symmetry operation9_654y+1,z,x-11
crystal symmetry operation16_555x,-y+1/2,-z+1/21
crystal symmetry operation18_665z+1,-x+3/2,-y+1/21
crystal symmetry operation23_656y+1,-z+1/2,-x+3/21
crystal symmetry operation27_755-x+5/2,y,-z+1/21
crystal symmetry operation32_645-z+3/2,x-1,-y+1/21
crystal symmetry operation34_656-y+3/2,z,-x+3/21
crystal symmetry operation38_755-x+5/2,-y+1/2,z1
crystal symmetry operation43_665-z+3/2,-x+3/2,y1
crystal symmetry operation48_654-y+3/2,-z+1/2,x-11
Buried area27580 Å2
ΔGint-68 kcal/mol
Surface area60650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.390, 125.390, 125.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-298-

HOH

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Components

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


Mass: 15985.019 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: aroQ, aroQ1, PA4846 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: O30557, 3-dehydroquinate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8M potassium sodium tartarate and 0.1M Sodium HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7362→31.35 Å / Num. all: 16975 / Num. obs: 16975 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 41.8 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 31.2
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 6.96 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.204 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→31.35 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.163 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19185 860 5.1 %RANDOM
Rwork0.16129 ---
obs0.16268 16108 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.983 Å2
Baniso -1Baniso -2Baniso -3
1--7.58 Å2-1.24 Å2-6.86 Å2
2---7.86 Å25.68 Å2
3---15.44 Å2
Refinement stepCycle: LAST / Resolution: 1.74→31.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 0 113 1187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191101
X-RAY DIFFRACTIONr_bond_other_d0.0020.021064
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.9451496
X-RAY DIFFRACTIONr_angle_other_deg0.98732426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4623.33354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58515177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.924159
X-RAY DIFFRACTIONr_chiral_restr0.1360.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021266
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02271
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_it2.3042.226555
X-RAY DIFFRACTIONr_mcbond_other2.2972.221554
X-RAY DIFFRACTIONr_mcangle_it3.2793.313692
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2422.605546
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.781 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 74 -
Rwork0.39 1143 -
obs--100 %

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