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- PDB-5uxm: Type II DAH7PS from Pseudomonas aeruginosa with Trp bound -

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Basic information

Entry
Database: PDB / ID: 5uxm
TitleType II DAH7PS from Pseudomonas aeruginosa with Trp 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 / TRYPTOPHAN / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 1.1May 2, 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 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2019Group: Derived calculations
Category: pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Revision 1.4Oct 4, 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,8898
Polymers50,1971
Non-polymers6927
Water5,765320
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)203,55832
Polymers200,7904
Non-polymers2,76828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Buried area12430 Å2
ΔGint-231 kcal/mol
Surface area60700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.680, 100.370, 115.600
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-504-

PO4

21A-920-

HOH

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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) magic
References: UniProt: Q9I000, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 6 types, 327 molecules

#2: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE


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


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.13 % / Description: rectangular 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 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: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2016
RadiationMonochromator: Double Crystal SI(111) water cooled sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.54→75.79 Å / Num. obs: 70122 / % possible obs: 99.6 % / Redundancy: 7 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.044 / Net I/σ(I): 9.3
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.122 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3437 / CC1/2: 0.702 / Rpim(I) all: 0.452 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B7O

2b7o


Resolution: 1.54→75.79 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.782 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21039 3546 5.1 %RANDOM
Rwork0.18479 ---
obs0.1861 66588 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.135 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.98 Å2
Refinement stepCycle: 1 / Resolution: 1.54→75.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 38 320 3787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193692
X-RAY DIFFRACTIONr_bond_other_d0.0020.023412
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9485034
X-RAY DIFFRACTIONr_angle_other_deg0.9513.0017822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9225479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00723.626182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64115591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0981533
X-RAY DIFFRACTIONr_chiral_restr0.0860.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214377
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02906
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_it1.3321.9071862
X-RAY DIFFRACTIONr_mcbond_other1.331.9071861
X-RAY DIFFRACTIONr_mcangle_it2.1952.8552350
X-RAY DIFFRACTIONr_mcangle_other2.1952.8552351
X-RAY DIFFRACTIONr_scbond_it1.762.0621830
X-RAY DIFFRACTIONr_scbond_other1.762.0581822
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8223.0182669
X-RAY DIFFRACTIONr_long_range_B_refined4.62216.024508
X-RAY DIFFRACTIONr_long_range_B_other4.42215.5194330
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 278 -
Rwork0.27 4861 -
obs--99.84 %

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