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- PDB-2ysw: Crystal Structure of the 3-dehydroquinate dehydratase from Aquife... -

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Basic information

Entry
Database: PDB / ID: 2ysw
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
3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsTanaka, T. / Kumarevel, T.S. / Ebihara, A. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Wang, B.C. / 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: Kumarevel, T.S. / Tanaka, T. / Kuramitsu, S. / Yokoyama, S.
History
DepositionApr 4, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 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


Theoretical massNumber of molelcules
Total (without water)75,0143
Polymers75,0143
Non-polymers00
Water4,161231
1
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase


Theoretical massNumber of molelcules
Total (without water)50,0102
Polymers50,0102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-19 kcal/mol
Surface area17990 Å2
MethodPISA, PQS
2
C: 3-dehydroquinate dehydratase

C: 3-dehydroquinate dehydratase


Theoretical massNumber of molelcules
Total (without water)50,0102
Polymers50,0102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)131.796, 131.796, 108.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 25004.783 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL-X / References: UniProt: O66440, 3-dehydroquinate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 3.13 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 291 K / Method: liquid diffusion / pH: 4.8
Details: 44% MPD, 0.1M Acetate NaOH, 0.05M Magnesium chloride, pH 4.80, LIQUID DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.979
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2007
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 45453 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 26.4 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.318 / % possible all: 93.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EGZ

2egz


Resolution: 2.25→19.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4015365.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2239 5 %RANDOM
Rwork0.218 ---
obs0.218 45179 99.1 %-
all-45453 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.12 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 43.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5277 0 0 231 5508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 334 4.7 %
Rwork0.248 6782 -
obs--95.2 %
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

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