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- PDB-5hue: DAHP synthase from Corynebacterium glutamicum in complex with try... -

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Basic information

Entry
Database: PDB / ID: 5hue
TitleDAHP synthase from Corynebacterium glutamicum in complex with tryptophan
Components3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
KeywordsSUGAR BINDING PROTEIN / DAHP synthase / shikimate pathway
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
DAHP synthetase, class II / Class-II DAHP synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / PHOSPHOENOLPYRUVATE / TRIETHYLENE GLYCOL / PHOSPHATE ION / TRYPTOPHAN / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsBurschowsky, D. / Heim, J.B. / Thorbjoernsrud, H.V. / Krengel, U.
Funding support Norway, 1items
OrganizationGrant numberCountry
The Research Council of Norway214037 Norway
CitationJournal: Biochemistry / Year: 2018
Title: Inter-Enzyme Allosteric Regulation of Chorismate Mutase in Corynebacterium glutamicum: Structural Basis of Feedback Activation by Trp.
Authors: Burschowsky, D. / Thorbjornsrud, H.V. / Heim, J.B. / Fahrig-Kamarauskaite, J.R. / Wurth-Roderer, K. / Kast, P. / Krengel, U.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 10, 2024Group: 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-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,63113
Polymers52,1501
Non-polymers1,48012
Water37821
1
A: 3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
hetero molecules

A: 3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
hetero molecules

A: 3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
hetero molecules

A: 3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,52352
Polymers208,6024
Non-polymers5,92148
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area19490 Å2
ΔGint-276 kcal/mol
Surface area63250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.189, 109.189, 279.897
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-603-

HOH

21A-621-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase


Mass: 52150.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: Cgl2178 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NNL5

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Non-polymers , 8 types, 33 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.62 Å3/Da / Density % sol: 73.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 100 mM NH4 formate, pH 6.6, 100 mM KSCN, 30% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.65→37.01 Å / Num. obs: 29830 / % possible obs: 99.7 % / Redundancy: 17.36 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 9.39
Reflection shellResolution: 2.65→2.8 Å / Redundancy: 17.85 % / Rmerge(I) obs: 7.276 / Mean I/σ(I) obs: 0.39 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B7O

2b7o


Resolution: 2.65→37.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 15.656 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28463 1436 4.9 %RANDOM
Rwork0.24675 ---
obs0.24857 28128 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 108.112 Å2
Baniso -1Baniso -2Baniso -3
1-3.61 Å21.81 Å20 Å2
2--3.61 Å20 Å2
3----11.73 Å2
Refinement stepCycle: 1 / Resolution: 2.65→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 94 21 3571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193613
X-RAY DIFFRACTIONr_bond_other_d0.0030.023415
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.9764896
X-RAY DIFFRACTIONr_angle_other_deg0.92137833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1225446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51824.08174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25115581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.41530
X-RAY DIFFRACTIONr_chiral_restr0.0640.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02811
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_it3.78310.7661791
X-RAY DIFFRACTIONr_mcbond_other3.78410.7661789
X-RAY DIFFRACTIONr_mcangle_it6.11716.1552234
X-RAY DIFFRACTIONr_mcangle_other6.11616.1542235
X-RAY DIFFRACTIONr_scbond_it3.41611.081822
X-RAY DIFFRACTIONr_scbond_other3.41111.081822
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7316.5052663
X-RAY DIFFRACTIONr_long_range_B_refined9.1984.3863953
X-RAY DIFFRACTIONr_long_range_B_other9.19284.3913954
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.536 110 -
Rwork0.562 2012 -
obs--100 %

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