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- PDB-5uxn: Type II DAH7PS from Pseudomonas aeruginosa with Tyr bound -

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Basic information

Entry
Database: PDB / ID: 5uxn
TitleType II DAH7PS from Pseudomonas aeruginosa with Tyr bound
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / DAH7PS / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / shikimate pathway
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aromatic amino acid family biosynthetic process
Similarity search - Function
DAHP synthetase, class II / Class-II DAHP synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / PHOSPHOENOLPYRUVATE / PHOSPHATE ION / TYROSINE / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsSterritt, O.W. / Jameson, G.B. / Parker, E.J.
CitationJournal: Biochemistry / Year: 2018
Title: A Pseudoisostructural Type II DAH7PS Enzyme from Pseudomonas aeruginosa: Alternative Evolutionary Strategies to Control Shikimate Pathway Flux.
Authors: Sterritt, O.W. / Kessans, S.A. / Jameson, G.B. / Parker, E.J.
History
DepositionFeb 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / 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 1.2May 2, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.3May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.5Mar 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
A: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8317
Polymers50,1971
Non-polymers6346
Water2,558142
1
A: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules

A: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules

A: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules

A: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,32428
Polymers200,7904
Non-polymers2,53424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area12320 Å2
ΔGint-203 kcal/mol
Surface area60580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.270, 100.540, 115.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-501-

PO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phospho-2-dehydro-3-deoxyheptonate aldolase


Mass: 50197.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA2843 / Plasmid: pET28a / Details (production host): N-terminal His tag + linker / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9I000, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 6 types, 148 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P
#5: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.35 Å3/Da / Density % sol: 47.68 % / Description: rod
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium acetate pH 5.5, 0.8 M sodium formate, 1 mM cobalt chloride, 1 mM phosphoenol pyruvate, 3 mM Tyr, 26 % PEG 2000 MME
Temp details: Temperature controlled

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2016
RadiationMonochromator: Double Crystal SI(111) water cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→57.63 Å / Num. obs: 24329 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 13.3 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.056 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 6.4 / Num. unique obs: 2093 / CC1/2: 0.936 / Rpim(I) all: 0.13 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2.2→57.63 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.313 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.2 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22671 1205 4.9 %RANDOM
Rwork0.18194 ---
obs0.18414 23206 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 2.2→57.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 35 142 3611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193552
X-RAY DIFFRACTIONr_bond_other_d0.0060.023307
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9514820
X-RAY DIFFRACTIONr_angle_other_deg0.98737565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9545448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1823.543175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03315568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.951532
X-RAY DIFFRACTIONr_chiral_restr0.0950.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214129
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02863
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_it2.2822.3121786
X-RAY DIFFRACTIONr_mcbond_other2.282.3121785
X-RAY DIFFRACTIONr_mcangle_it3.4853.4562230
X-RAY DIFFRACTIONr_mcangle_other3.4843.4562231
X-RAY DIFFRACTIONr_scbond_it2.7992.5071764
X-RAY DIFFRACTIONr_scbond_other2.7992.5071764
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3573.6592588
X-RAY DIFFRACTIONr_long_range_B_refined6.02817.8344013
X-RAY DIFFRACTIONr_long_range_B_other6.02817.8354014
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 84 -
Rwork0.222 1691 -
obs--99.94 %

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