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- PDB-5hpq: Crystal structure of cyclohexadienyl dehydratase from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 5hpq
TitleCrystal structure of cyclohexadienyl dehydratase from Pseudomonas aeruginosa bound to acetate
ComponentsCyclohexadienyl dehydratase
KeywordsLYASE / phenylalanine biosynthesis / cyclohexadienyl dehydratase / periplasmic binding protein
Function / homology
Function and homology information


arogenate dehydratase / arogenate dehydratase activity / prephenate dehydratase / prephenate dehydratase activity / L-phenylalanine biosynthetic process / periplasmic space
Similarity search - Function
Cyclohexadienyl dehydratase PheC / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Cyclohexadienyl dehydratase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsClifton, B.E. / Carr, P.D. / Jackson, C.J.
CitationJournal: To Be Published
Title: Crystal structure of cyclohexadienyl dehydratase from Pseudomonas aeruginosa bound to acetate
Authors: Clifton, B.E. / Kaczmarski, J.A. / Carr, P.D. / Jackson, C.J.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 20, 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: Cyclohexadienyl dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4082
Polymers29,3491
Non-polymers591
Water99155
1
A: Cyclohexadienyl dehydratase
hetero molecules

A: Cyclohexadienyl dehydratase
hetero molecules

A: Cyclohexadienyl dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2256
Polymers88,0483
Non-polymers1773
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)124.890, 124.890, 40.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Cyclohexadienyl dehydratase


Mass: 29349.311 Da / Num. of mol.: 1 / Fragment: UNP residues 26-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pheC, PA3475 / Plasmid: pDOTS7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q01269, prephenate dehydratase, arogenate dehydratase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 1 uL 10 mg/mL protein (20 mM TRIS pH 8.0, 100 mM NaCl, 0.5 mM DTT, 10% glycerol) + 1 uL 18% PEG 3350, 0.2 M ammonium acetate, 0.1 M TRIS pH 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 30, 2014
RadiationMonochromator: Silicon double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.05→38.03 Å / Num. obs: 14471 / % possible obs: 97.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.3
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 1.6 / % possible all: 82.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLM7.0.9data reduction
Aimless0.1.29data scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KBR

3kbr


Resolution: 2.05→36.05 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.736 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24099 727 5 %RANDOM
Rwork0.17589 ---
obs0.17913 13739 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.129 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.05→36.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 4 55 1929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191918
X-RAY DIFFRACTIONr_bond_other_d0.0010.021796
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9552607
X-RAY DIFFRACTIONr_angle_other_deg0.8833.0014108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4265237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58123.69692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44715308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6851515
X-RAY DIFFRACTIONr_chiral_restr0.1050.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212198
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02455
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_it2.582.936952
X-RAY DIFFRACTIONr_mcbond_other2.5532.933950
X-RAY DIFFRACTIONr_mcangle_it3.6724.3921187
X-RAY DIFFRACTIONr_mcangle_other3.6794.3951188
X-RAY DIFFRACTIONr_scbond_it2.9813.172966
X-RAY DIFFRACTIONr_scbond_other2.9793.171967
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4154.6611421
X-RAY DIFFRACTIONr_long_range_B_refined5.87223.0722147
X-RAY DIFFRACTIONr_long_range_B_other5.84523.0622135
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.051→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 29 -
Rwork0.272 856 -
obs--82.25 %

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