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- PDB-1ujn: Crystal structure of dehydroquinate synthase from Thermus thermop... -

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Basic information

Entry
Database: PDB / ID: 1ujn
TitleCrystal structure of dehydroquinate synthase from Thermus thermophilus HB8
Componentsdehydroquinate synthase
KeywordsLYASE / dehydroquinate synthase / Thermus thermophilus / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


3-dehydroquinate synthase / 3-dehydroquinate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
3-dehydroquinate synthase family / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...3-dehydroquinate synthase family / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-dehydroquinate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSugahara, M. / Yokoyama, S. / Kuramitsu, S. / Miyano, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of dehydroquinate synthase from Thermus thermophilus HB8 showing functional importance of the dimeric state.
Authors: Sugahara, M. / Nodake, Y. / Sugahara, M. / Kunishima, N.
History
DepositionAug 6, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: dehydroquinate synthase
B: dehydroquinate synthase


Theoretical massNumber of molelcules
Total (without water)75,1182
Polymers75,1182
Non-polymers00
Water11,620645
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-12 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.403, 71.787, 71.636
Angle α, β, γ (deg.)90.00, 99.44, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

#1: Protein dehydroquinate synthase


Mass: 37559.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P83703, 3-dehydroquinate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 1.99 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.6 / Details: PEG 4000, pH 5.6, MICROBATCH, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120.0 mg/mlprotein1drop
212.5 %(w/v)PEG40001reservoir
30.1 MMES-NaOH1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 28, 2002 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 58577 / Num. obs: 58577 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.71 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.035 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.72 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 3.35 / Num. unique all: 5792 / Rsym value: 0.417 / % possible all: 99
Reflection
*PLUS
Num. measured all: 217026 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 99 % / Mean I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DQS

1dqs


Resolution: 1.8→37.2 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2944 -RANDOM
Rwork0.202 ---
all0.203 58489 --
obs0.203 58489 99 %-
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å2-2.02 Å2
2---2.44 Å20 Å2
3---3.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5120 0 0 645 5765
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.29 299 -
Rwork0.26 --
obs-5498 99 %
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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