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- PDB-1d0i: CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COE... -

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Basic information

Entry
Database: PDB / ID: 1d0i
TitleCRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COELICOLOR COMPLEXED WITH PHOSPHATE IONS
ComponentsTYPE II 3-DEHYDROQUINATE HYDRATASE
KeywordsLYASE / TYPE II DEHYDROQUINASE / SHIKIMATE PATHWAY / DODECAMERIC QUATERNARY STRUCTURE / TETRAHEDRAL SYMMETRY
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
PHOSPHATE ION / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsRoszak, A.W. / Krell, T. / Hunter, I.S. / Coggins, J.R. / Lapthorn, A.J.
CitationJournal: Structure / Year: 2002
Title: The structure and mechanism of the type II dehydroquinase from Streptomyces coelicolor.
Authors: Roszak, A.W. / Robinson, D.A. / Krell, T. / Hunter, I.S. / Fredrickson, M. / Abell, C. / Coggins, J.R. / Lapthorn, A.J.
History
DepositionSep 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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: TYPE II 3-DEHYDROQUINATE HYDRATASE
B: TYPE II 3-DEHYDROQUINATE HYDRATASE
C: TYPE II 3-DEHYDROQUINATE HYDRATASE
D: TYPE II 3-DEHYDROQUINATE HYDRATASE
E: TYPE II 3-DEHYDROQUINATE HYDRATASE
F: TYPE II 3-DEHYDROQUINATE HYDRATASE
G: TYPE II 3-DEHYDROQUINATE HYDRATASE
H: TYPE II 3-DEHYDROQUINATE HYDRATASE
I: TYPE II 3-DEHYDROQUINATE HYDRATASE
J: TYPE II 3-DEHYDROQUINATE HYDRATASE
K: TYPE II 3-DEHYDROQUINATE HYDRATASE
L: TYPE II 3-DEHYDROQUINATE HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,84332
Polymers198,83512
Non-polymers2,00820
Water36,4442023
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30740 Å2
ΔGint-186 kcal/mol
Surface area56540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.2, 137.5, 140.2
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
TYPE II 3-DEHYDROQUINATE HYDRATASE


Mass: 16569.605 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Description: STREPTOMYCES COELICOLOR / Plasmid: PDHQ / Production host: Escherichia coli (E. coli) / References: UniProt: P15474, 3-dehydroquinate dehydratase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2023 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 8000, SODIUM/POTASSIUM PHOSPHATE, TRIS BUFFER, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal
*PLUS
Density % sol: 57.1 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris11
210-20 %PEG800011
30.2 Msodium potassium phosphate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.89
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 1.8→45.03 Å / Num. all: 199360 / Num. obs: 199360 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.6
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.593 / % possible all: 93.5
Reflection
*PLUS
Num. measured all: 798417
Reflection shell
*PLUS
% possible obs: 93.5 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→45.03 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: USED RESTRAINED REFINEMENT OF THE MAXIMUM LIKELIHOOD RESIDUAL WITH THE SPARSE MATRIX AND INDIVIDUAL ATOM ANISOTROPIC B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 18324 9.2 %THE SAME REFLECTIONS WERE USED AS IN THE FIRST 2.7A-DATASET USED FOR THE STRUCTURE SOLUTION, EXTENDED TO 1.8A RESOLUTION OF THE PRESENT DATASET.
Rwork0.171 ---
all0.176 199360 --
obs0.176 199360 98.7 %-
Refinement stepCycle: LAST / Resolution: 1.8→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13827 0 112 2023 15962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.2 % / Rfactor obs: 0.149 / Rfactor Rfree: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_deg1.8

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