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- PDB-1gu1: Crystal structure of type II dehydroquinase from Streptomyces coe... -

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Basic information

Entry
Database: PDB / ID: 1gu1
TitleCrystal structure of type II dehydroquinase from Streptomyces coelicolor complexed with 2,3-anhydro-quinic acid
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / SHIKIMATE PATHWAY / 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
2,3 -ANHYDRO-QUINIC ACID / L(+)-TARTARIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRoszak, A.W. / Robinson, D.A. / 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
DepositionJan 22, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 24, 2013Group: Data collection / Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
B: 3-DEHYDROQUINATE DEHYDRATASE
C: 3-DEHYDROQUINATE DEHYDRATASE
D: 3-DEHYDROQUINATE DEHYDRATASE
E: 3-DEHYDROQUINATE DEHYDRATASE
F: 3-DEHYDROQUINATE DEHYDRATASE
G: 3-DEHYDROQUINATE DEHYDRATASE
H: 3-DEHYDROQUINATE DEHYDRATASE
I: 3-DEHYDROQUINATE DEHYDRATASE
J: 3-DEHYDROQUINATE DEHYDRATASE
K: 3-DEHYDROQUINATE DEHYDRATASE
L: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,32052
Polymers198,83512
Non-polymers5,48540
Water47,4522634
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40620 Å2
ΔGint-28.2 kcal/mol
Surface area53000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.600, 138.400, 141.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.00047, -0.91427, -0.4051), (0.42326, -0.3672, 0.82826), (-0.90601, -0.17107, 0.38714)77.03539, 2.44498, 57.0237
2given(-0.01781, 0.42808, -0.90356), (-0.90921, -0.38289, -0.16348), (-0.41595, 0.81862, 0.39604)50.4324, 81.51537, 7.71917
3given(-0.99994, 0.01046, 0.00236), (0.00862, 0.65349, 0.75689), (0.00638, 0.75687, -0.65354)59.50526, -17.51628, 37.92458
4given(0.003, -0.90209, -0.43153), (-0.40287, 0.39387, -0.82617), (0.91525, 0.17633, -0.36225)77.49197, 64.8762, 19.31279
5given(0.00661, -0.41953, 0.90772), (0.91001, -0.37377, -0.17938), (0.41453, 0.82722, 0.37931)9.04272, 26.91825, -16.78384
6given(0.00687, 0.90322, 0.42911), (-0.40192, -0.39044, 0.82826), (0.91565, -0.17816, 0.36034)-18.34674, 27.86117, 3.62359
7given(0.01189, 0.42154, -0.90673), (0.91336, 0.36449, 0.18143), (0.40697, -0.83033, -0.38069)50.01438, -12.76838, 70.20421
8given(-1, -0.00184, -0.00168), (0.00247, -0.65652, -0.7543), (0.00029, -0.75431, 0.65652)60.16796, 86.45656, 39.67637
9given(-0.01386, -0.43029, 0.90258), (-0.90801, 0.38342, 0.16885), (-0.41872, -0.81722, -0.39602)10.06746, 42.12491, 95.03992
10given(0.99995, -0.00838, 0.00473), (-0.00837, -0.99996, -0.002), (0.00475, 0.00196, -0.99999)0.05969, 69.64996, 77.52781
11given(0.00152, 0.91496, 0.40355), (0.42088, 0.36548, -0.83023), (-0.90712, 0.17111, -0.38453)-17.67109, 41.35124, 75.16728

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
3-DEHYDROQUINATE DEHYDRATASE / / TYPE II 3-DEHYDROQUINATE HYDRATASE / 3-DEHYDROQUINASE / TYPE II DHQASE


Mass: 16569.605 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Plasmid: PDHQ / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P15474, 3-dehydroquinate dehydratase

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Non-polymers , 5 types, 2674 molecules

#2: Chemical
ChemComp-FA1 / 2,3 -ANHYDRO-QUINIC ACID


Mass: 174.151 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C7H10O5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


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


Mass: 18.015 Da / Num. of mol.: 2634 / 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: 2.8 Å3/Da / Density % sol: 55.9 %
Crystal growpH: 8.5
Details: PEG 8000, SODIUM/POTASSIUM PHOSPHATE, TRIS BUFFER, pH 8.50

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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 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 1.8→70 Å / Num. obs: 648516 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.088
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 2.9 % / % possible all: 90.9

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DHQ

2dhq


Resolution: 1.8→22 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.2 20218 10 %RANDOM
Rwork0.155 ---
obs-202189 98.1 %-
Refinement stepCycle: LAST / Resolution: 1.8→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13452 0 368 2634 16454

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