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- PDB-1gtz: Structure of STREPTOMYCES COELICOLOR TYPE II DEHYDROQUINASE R23A ... -

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Basic information

Entry
Database: PDB / ID: 1gtz
TitleStructure of STREPTOMYCES COELICOLOR TYPE II DEHYDROQUINASE R23A MUTANT IN COMPLEX WITH DEHYDROSHIKIMATE
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / TYPE II DEHYDROQUINASE / SHIKIMATE PATHWAY / DODECAMERIC QUATERNARY STRUCTURE / TETRAHEDRAL SYMMETRY AROMATIC AMINO ACID BIOSYNTHESIS
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
3-DEHYDROSHIKIMATE / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRoszak, A.W. / Krell, T. / Robinson, D.A. / 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 1.0Jun 27, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
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)200,38028
Polymers197,80212
Non-polymers2,57816
Water28,4641580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.100, 136.200, 96.700
Angle α, β, γ (deg.)90.00, 101.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.44306, -0.73264, -0.51666), (0.8963, -0.37398, -0.2383), (-0.01863, -0.56866, 0.82236)34.18311, -8.61393, 4.32825
2given(-0.44224, 0.89656, -0.02455), (-0.73433, -0.37767, -0.56403), (-0.51496, -0.23141, 0.82539)23.23141, 24.16837, 11.9558
3given(-0.79879, 0.57817, -0.16629), (0.57312, 0.64726, -0.50259), (-0.18295, -0.49677, -0.84838)31.80264, 2.23186, 43.8085
4given(0.03599, -0.47654, 0.87842), (-0.88471, 0.39357, 0.24976), (-0.46474, -0.78614, -0.40744)-4.36874, 8.50438, 38.53534
5given(0.87266, 0.33224, -0.35788), (0.47111, -0.3799, 0.79607), (0.12853, -0.8633, -0.48804)10.02567, -24.60291, 31.05548
6given(0.87336, 0.46733, 0.13728), (0.34055, -0.38438, -0.85807), (-0.34823, 0.79615, -0.49485)-0.99157, 13.89276, 38.63177
7given(-0.45436, -0.33649, 0.82482), (0.74378, 0.36628, 0.55914), (-0.49026, 0.86753, 0.08385)4.45448, -23.58772, 27.96906
8given(-0.08636, -0.56543, -0.82026), (-0.56994, -0.64726, 0.50618), (-0.81713, 0.51122, -0.26636)35.14317, -2.36385, 40.75355
9given(0.01494, -0.89339, -0.44903), (-0.47767, 0.38815, -0.78814), (0.87841, 0.22626, -0.42095)25.48926, 25.17432, 17.83086
10given(-0.10546, -0.00852, 0.99439), (-0.009, -0.99991, -0.00953), (0.99438, -0.00995, 0.10537)-4.89023, 0.31988, 4.22976
11given(-0.45458, 0.74299, -0.49124), (-0.33232, 0.37022, 0.86747), (0.82639, 0.55758, 0.07862)33.7586, -13.94129, 7.62808

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Components

#1: Protein
3-DEHYDROQUINATE DEHYDRATASE /


Mass: 16483.488 Da / Num. of mol.: 12 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Plasmid: PTB-361 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P15474, 3-dehydroquinate dehydratase
#2: 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
#3: Chemical
ChemComp-DHK / 3-DEHYDROSHIKIMATE / 3-Dehydroshikimic acid


Mass: 174.151 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C7H10O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1580 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: CATALYSIS VIA AN ENOLATE FOR A TRANS-DEHYDRATION

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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: 2.9 Å3/Da / Density % sol: 56.5 %
Description: DATA PROCESSED TO CORNERS OF DETECTOR THEREFORE LOW COMPLETENESS OF HIGHEST RESOLUTION SHELL
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: 0.87
DetectorType: ADC QUANTUM 4 / Detector: CCD / Date: Mar 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 213906 / % possible obs: 98.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.064
Reflection shellResolution: 1.6→1.63 Å / % possible all: 21.5

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Processing

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

2dhq


Resolution: 1.6→45 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.221 -10 %RANDOM
Rwork0.179 ---
obs-213906 73.8 %-
Refinement stepCycle: LAST / Resolution: 1.6→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13380 0 176 1580 15136

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