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- PDB-1j2y: Crystal structure of the type II 3-dehydroquinase -

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Basic information

Entry
Database: PDB / ID: 1j2y
TitleCrystal structure of the type II 3-dehydroquinase
Components3-dehydroquinate dehydratase
KeywordsLYASE / 3-dehydroquinase
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
1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLee, B.I. / Kwak, J.E. / Suh, S.W.
CitationJournal: Proteins / Year: 2003
Title: Crystal structure of the type II 3-dehydroquinase from Helicobacter pylori
Authors: Lee, B.I. / Kwak, J.E. / Suh, S.W.
History
DepositionJan 15, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6892
Polymers18,4991
Non-polymers1901
Water34219
1
A: 3-dehydroquinate dehydratase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)224,27324
Polymers221,99112
Non-polymers2,28212
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_757-x+2,y,-z+21
crystal symmetry operation4_557x,-y,-z+21
crystal symmetry operation5_546z,x-1,y+11
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_766-z+2,-x+1,y+11
crystal symmetry operation8_746-z+2,x-1,-y+11
crystal symmetry operation9_645y+1,z-1,x1
crystal symmetry operation10_647-y+1,z-1,-x+21
crystal symmetry operation11_667y+1,-z+1,-x+21
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area31510 Å2
ΔGint-201 kcal/mol
Surface area75370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)98.910, 98.910, 98.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232
DetailsThe biological assembly is dodecamer generated from the monomer in the asymmetric unit by the operations: z, x-1, y+1 and y+1,z-1,x and -x+2, y, -z+2 and -y+1, z-1, -x+2 and -z+2,x-1,-y+1 and -z+2, -x+1, y+1 and -y+1,-z+1,x and -x+2,-y,z and y+1, -z+1, -x+2 and x, -y, -z+2 and z,-x+1, -y+1 and

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Components

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


Mass: 18499.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: aroQ / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q48255, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-DQA / 1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID / 3-DEHYDROQUINIC ACID / 3-Dehydroquinic acid


Mass: 190.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.3 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 4000, sodium cholride, sodium citrate, EDTA, 2-mercaptoethanol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: Kwak, J.E., (2001) Acta Crystallogr., D57, 279.
Components of the solutions
*PLUS
Conc.: 20 mg/ml / Common name: protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→44 Å / Num. all: 6146 / Num. obs: 6146 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 38 % / Biso Wilson estimate: 53.5 Å2 / Rsym value: 0.086
Reflection shellResolution: 2.5→2.64 Å / Rsym value: 0.484 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DHQ

2dhq


Resolution: 2.6→19.78 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 160671.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.272 558 10.9 %RANDOM
Rwork0.218 ---
obs0.218 5133 93.8 %-
all-5469 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.0261 Å2 / ksol: 0.311869 e/Å3
Displacement parametersBiso mean: 52.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 0 13 19 1253
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.511.5
X-RAY DIFFRACTIONc_mcangle_it6.532
X-RAY DIFFRACTIONc_scbond_it7.112
X-RAY DIFFRACTIONc_scangle_it8.62.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 77 10.7 %
Rwork0.338 642 -
obs--81.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3DHQ.PARAMDHQ.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
LS refinement shell
*PLUS
Highest resolution: 2.6 Å

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