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- PDB-1v1j: Crystal structure of type II Dehydroquintae Dehydratase from Stre... -

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Basic information

Entry
Database: PDB / ID: 1v1j
TitleCrystal structure of type II Dehydroquintae Dehydratase from Streptomyces coelicolor in complex with 3-fluoro
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / DHQ / SHIKIMATE / DEHYDROQUINASE / 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
2-ANHYDRO-3-FLUORO-QUINIC ACID / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRoszak, A.W. / Coggins, J.R. / Lapthorn, A.J.
CitationJournal: Org.Biomol.Chem. / Year: 2004
Title: (1R,4S,5R)-3-Fluoro-1,4,5-Trihydroxy-2-Cyclohexene-1-Carboxylic Acid: The Fluoro Analogue of the Enolate Intermediate in the Reaction Catalyzed by Type II Dehydroquinases
Authors: Frederickson, M. / Roszak, A.W. / Coggins, J.R. / Lapthorn, A.J. / Abell, C.
History
DepositionApr 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

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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)203,20428
Polymers200,41012
Non-polymers2,79416
Water12,611700
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)116.475, 138.941, 141.925
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(0.00045, 0.40446, -0.91456), (-0.91487, -0.36909, -0.16368), (-0.40376, 0.83677, 0.36986)51.89528, 82.1555, 7.52426
2given(-0.00049, -0.91224, -0.40967), (0.40708, -0.37437, 0.83315), (-0.91339, -0.16636, 0.37153)78.43419, 3.41615, 58.11004
3given(-0.99998, -0.00158, -0.0054), (-0.00506, 0.67159, 0.74091), (0.00245, 0.74092, -0.67159)62.43271, -16.7569, 38.04821
4given(0.00331, -0.40249, 0.91542), (-0.91371, 0.37077, 0.16632), (-0.40635, -0.83698, -0.36653)9.98314, 43.82185, 93.83305
5given(-0.00316, 0.91409, 0.4055), (-0.40276, -0.37232, 0.83616), (0.9153, -0.16068, 0.36934)-16.11196, 28.32615, 1.31071
6given(-0.0034, -0.40592, 0.9139), (0.91439, -0.37123, -0.16148), (0.40481, 0.83511, 0.37244)10.32446, 25.43354, -17.56244
7given(0.00329, 0.91282, 0.40834), (0.40332, 0.37245, -0.83583), (-0.91505, 0.16744, -0.36694)-16.36827, 41.22469, 74.78658
8given(-0.99999, 0.00385, -0.00119), (-0.0017, -0.67058, -0.74184), (-0.00366, -0.74183, 0.67058)61.97967, 86.44312, 38.55089
9given(-0.00334, -0.91443, -0.40473), (-0.40617, 0.37109, -0.83506), (0.91379, 0.1616, -0.37265)78.41739, 66.3082, 18.52069
10given(0.99999, 0.00164, 0.00488), (0.00165, -1, -0.0015), (0.00487, 0.00151, -0.99999)-0.21171, 69.54708, 76.21187
11given(-0.00288, 0.40691, -0.91346), (0.91528, 0.36902, 0.1615), (0.4028, -0.83561, -0.3735)51.92285, -12.54626, 69.01919

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Components

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


Mass: 16700.801 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Plasmid: PTB361 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P15474, 3-dehydroquinate dehydratase
#2: Chemical
ChemComp-FA3 / 2-ANHYDRO-3-FLUORO-QUINIC ACID


Mass: 192.142 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C7H9FO5
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 3 Å3/Da / Density % sol: 58.5 %
Crystal growpH: 7.5 / Details: PEG 8000, NA/K PHOSPHATE, TRIS BUFFER, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 15, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 113346 / % possible obs: 96.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 25.11 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.97
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.85 / % possible all: 99.5

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GUO

1guo


Resolution: 2.2→20 Å / SU B: 9.91074 / SU ML: 0.24061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.34862 / ESU R Free: 0.22984
RfactorNum. reflection% reflectionSelection details
Rfree0.23811 10066 12 %RANDOM
Rwork0.2151 ---
obs0.21745 89858 85.3 %-
Displacement parametersBiso mean: 25.126 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20 Å2
2---1.15 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13488 0 188 700 14376

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