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- PDB-2egz: Crystal structure of the 3-dehydroquinate dehydratase from Aquife... -

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Basic information

Entry
Database: PDB / ID: 2egz
TitleCrystal structure of the 3-dehydroquinate dehydratase from Aquifex aeolicus VF5
Components3-dehydroquinate dehydratase
KeywordsLYASE / 3-dehydroquinate dehydratase / Aquifex aeolicus VF5 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
L(+)-TARTARIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsKarthe, P. / Kumarevel, T.S. / Ebihara, A. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the 3-dehydroquinate dehydratase from Aquifex aeolicus VF5
Authors: Karthe, P. / Kumarevel, T.S. / Ebihara, A. / Kuramitsu, S. / Yokoyama, S.
History
DepositionMar 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3104
Polymers50,0102
Non-polymers3002
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.937, 67.614, 60.238
Angle α, β, γ (deg.)90.00, 99.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25004.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aroD / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL-X / References: UniProt: O66440, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.13 Å3/Da / Density % sol: 42.18 % / Description: the file contains Friedel pairs
Crystal growTemperature: 291 K / Method: liquid diffusion / pH: 5.6
Details: 30% PEG 4000, 0.2M Ammonium acetate, 0.1M Citrate pH5.6, LIQUID DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9788, 0.900, 0.9794
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 15, 2006
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.91
30.97941
ReflectionResolution: 1.75→50 Å / Num. obs: 80554 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.287 / Num. unique all: 3944 / % possible all: 94.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→19.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 123083.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2269 2.9 %RANDOM
Rwork0.22 ---
obs0.22 77918 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.75 Å2 / ksol: 0.404824 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.78 Å20 Å22.66 Å2
2---3.22 Å20 Å2
3----0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.75→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 20 123 3585
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 318 2.9 %
Rwork0.266 10711 -
obs--79.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.param
X-RAY DIFFRACTION4ion.paramion.param
X-RAY DIFFRACTION5tla_xplor_partla_xplor_top

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