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- PDB-5swv: Dehydroquinate dehydratase and shikimate dehydrogenase from S. po... -

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Basic information

Entry
Database: PDB / ID: 5swv
TitleDehydroquinate dehydratase and shikimate dehydrogenase from S. pombe AroM
ComponentsPentafunctional AROM polypeptide
KeywordsLYASE / enzyme / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate dehydrogenase (NADP+) / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity ...3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate dehydrogenase (NADP+) / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Pentafunctional AroM protein / Shikimate dehydrogenase, AroM-type / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate kinase/Threonine synthase-like 1 / Shikimate kinase/gluconokinase / Shikimate kinase ...Pentafunctional AroM protein / Shikimate dehydrogenase, AroM-type / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate kinase/Threonine synthase-like 1 / Shikimate kinase/gluconokinase / Shikimate kinase / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / Shikimate dehydrogenase substrate binding, N-terminal / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / Shikimate dehydrogenase substrate binding domain / EPSP synthase signature 2. / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / Leucine Dehydrogenase, chain A, domain 1 / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Aldolase class I / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily / TIM Barrel / Alpha-Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Pentafunctional AROM polypeptide
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLight, S.H. / Minasov, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Dehydroquinate dehydratase and shikimate dehydrogenase from S. pombe AroM
Authors: Light, S.H. / Minasov, G. / Anderson, W.F.
History
DepositionAug 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Pentafunctional AROM polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7193
Polymers59,4191
Non-polymers3002
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.797, 121.797, 191.851
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11C-1781-

HOH

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Components

#1: Protein Pentafunctional AROM polypeptide


Mass: 59419.031 Da / Num. of mol.: 1 / Fragment: UNP residues 1043-1573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: aro1, SPAC1834.02 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P7R0, 3-dehydroquinate synthase, 3-phosphoshikimate 1-carboxyvinyltransferase, shikimate kinase, 3-dehydroquinate dehydratase, shikimate dehydrogenase (NADP+)
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: Protein: 6.0 mg/ml, 10 mM Tris (pH 8.3), 1 mM TCEP Crystallization condition 0.2 M Potassium thiocynate and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 24880 / % possible obs: 99.4 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.197 / Net I/σ(I): 12.9
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.778 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 22.791 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.428 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23279 1247 5 %RANDOM
Rwork0.19442 ---
obs0.19632 23620 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.259 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20.61 Å20 Å2
2--1.22 Å20 Å2
3----3.96 Å2
Refinement stepCycle: 1 / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4172 0 20 93 4285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194281
X-RAY DIFFRACTIONr_bond_other_d0.0020.024152
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9745808
X-RAY DIFFRACTIONr_angle_other_deg0.91239562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61624.066182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4715739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5621525
X-RAY DIFFRACTIONr_chiral_restr0.0730.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02946
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2673.5212118
X-RAY DIFFRACTIONr_mcbond_other1.2663.522117
X-RAY DIFFRACTIONr_mcangle_it2.2875.282647
X-RAY DIFFRACTIONr_mcangle_other2.2875.2822648
X-RAY DIFFRACTIONr_scbond_it1.2523.7112162
X-RAY DIFFRACTIONr_scbond_other1.253.7112162
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2555.4833162
X-RAY DIFFRACTIONr_long_range_B_refined3.78827.2774641
X-RAY DIFFRACTIONr_long_range_B_other3.78827.2844642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.653→2.722 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 92 -
Rwork0.325 1631 -
obs--95.19 %
Refinement TLS params.Method: refined / Origin x: 27.2442 Å / Origin y: 54.3232 Å / Origin z: 103.2401 Å
111213212223313233
T0.1072 Å20.0162 Å2-0.0024 Å2-0.1423 Å2-0.0043 Å2--0.0006 Å2
L0.3685 °2-0.0223 °2-0.2118 °2-0.0318 °2-0.0347 °2--0.2653 °2
S0.0002 Å °-0.0564 Å °0.0107 Å °-0.0254 Å °0.0105 Å °0.002 Å °-0.0356 Å °0.0237 Å °-0.0107 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1044 - 1289
2X-RAY DIFFRACTION1C1290 - 1414
3X-RAY DIFFRACTION1C1415 - 1525
4X-RAY DIFFRACTION1C1526 - 1573

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