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- PDB-2yr1: Crystal Structure of 3-dehydroquinate dehydratase from Geobacillu... -

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Basic information

Entry
Database: PDB / ID: 2yr1
TitleCrystal Structure of 3-dehydroquinate dehydratase from Geobacillus kaustophilus HTA426
Components3-dehydroquinate dehydratase
KeywordsLYASE / amino acid biosynthesis / 3-dehydroquinase / 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 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 speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKagawa, W. / Kurumizaka, H. / Bessho, Y. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Wang, B.C. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Crystal Structure of 3-dehydroquinate dehydratase from Geobacillus kaustophilus HTA426
Authors: Kagawa, W. / Kurumizaka, H. / Bessho, Y. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Wang, B.C. / Yokoyama, S.
History
DepositionApr 1, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 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

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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


Theoretical massNumber of molelcules
Total (without water)57,1942
Polymers57,1942
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-23 kcal/mol
Surface area20770 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.309, 76.642, 86.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly is unknown.

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Components

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


Mass: 28596.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Plasmid: pET-HisTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q5KY94, 3-dehydroquinate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 293 K / Method: micro batch (by tera) / pH: 4.6
Details: 1M 1,6 hexanediol, 0.01M cobaltous chloride hexahydrate, 0.1M sodium acetate trihydrate, pH 4.6, micro batch (by TERA), temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97901 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2007
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 32360 / Num. obs: 32320 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 24
Reflection shellResolution: 2→2.07 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 20.4 / Num. unique all: 3171 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QFE

1qfe


Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 3220 -random
Rwork0.234 ---
all0.292 32238 --
obs0.234 29018 99.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4008 0 0 169 4177
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00933
X-RAY DIFFRACTIONc_angle_d1.49
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d1.03
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
2-2.070.3253170.244X-RAY DIFFRACTION285810
2.07-2.150.3173370.23X-RAY DIFFRACTION281110
2.15-2.250.3123390.244X-RAY DIFFRACTION286310
2.25-2.370.3442980.249X-RAY DIFFRACTION288410
2.37-2.520.3123110.234X-RAY DIFFRACTION287910
2.52-2.710.3093270.245X-RAY DIFFRACTION289810
2.71-2.990.2923350.239X-RAY DIFFRACTION286210
2.99-3.420.2952970.245X-RAY DIFFRACTION293510
3.42-4.310.2713360.224X-RAY DIFFRACTION295510
4.31-500.2613230.223X-RAY DIFFRACTION307310

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