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- PDB-2qmx: The crystal structure of L-Phe inhibited prephenate dehydratase f... -

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Basic information

Entry
Database: PDB / ID: 2qmx
TitleThe crystal structure of L-Phe inhibited prephenate dehydratase from Chlorobium tepidum TLS
ComponentsPrephenate dehydratase
KeywordsLIGASE / APC86053 / L-Phe inhibition / prephenate dehydratase / PDT / Chlorobium tepidum TLS / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Lyase
Function / homology
Function and homology information


prephenate dehydratase / prephenate dehydratase activity / chorismate mutase activity / L-phenylalanine biosynthetic process
Similarity search - Function
Prephenate dehydratase signature 2. / Bifunctional P-protein, chorismate mutase/prephenate dehydratase / Prephenate dehydratase, conserved site / Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / ACT domain / ACT domain / ACT domain profile. / ACT domain ...Prephenate dehydratase signature 2. / Bifunctional P-protein, chorismate mutase/prephenate dehydratase / Prephenate dehydratase, conserved site / Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / ACT domain / ACT domain / ACT domain profile. / ACT domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHENYLALANINE / Prephenate dehydratase
Similarity search - Component
Biological speciesChlorobium tepidum TLS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsTan, K. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Struct.Biol. / Year: 2008
Title: Structures of open (R) and close (T) states of prephenate dehydratase (PDT) - implication of allosteric regulation by L-phenylalanine.
Authors: Tan, K. / Li, H. / Zhang, R. / Gu, M. / Clancy, S.T. / Joachimiak, A.
History
DepositionJul 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prephenate dehydratase
B: Prephenate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,32417
Polymers63,1922
Non-polymers1,13115
Water68538
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
MethodPISA
2
A: Prephenate dehydratase
B: Prephenate dehydratase
hetero molecules

A: Prephenate dehydratase
B: Prephenate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,64734
Polymers126,3854
Non-polymers2,26230
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)86.870, 127.886, 56.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsChains A and B form a dimer. The dimer and its symmetry-related dimer (-x,-y,z) form a tetramer.

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Components

#1: Protein Prephenate dehydratase /


Mass: 31596.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum TLS (bacteria) / Species: Chlorobaculum tepidum / Strain: TLS, DSM 12025 / Gene: pheA, CT1666 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8KBW6, prephenate dehydratase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% v/v PEG 400, 0.1M Acetate, 0.2M Calcium Acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918, 0.97932
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2007 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.979321
ReflectionResolution: 2.3→41.13 Å / Num. all: 23798 / Num. obs: 23798 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 35.5
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1245 / % possible all: 52.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→41.13 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.895 / SU B: 17.822 / SU ML: 0.21 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.547 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28899 1347 5.7 %RANDOM
Rwork0.21916 ---
all0.22306 22409 --
obs0.22306 22409 82.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.497 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å20 Å2
2--4.75 Å20 Å2
3----3.14 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 76 38 4472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224528
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2881.9596116
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.895556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90323.945218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.33415736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8241530
X-RAY DIFFRACTIONr_chiral_restr0.1680.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023478
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2540.22201
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.22946
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2193
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0461.52885
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66724478
X-RAY DIFFRACTIONr_scbond_it2.76731861
X-RAY DIFFRACTIONr_scangle_it3.9984.51637
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 53 -
Rwork0.212 897 -
obs--45.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.04291.27480.07875.69671.00360.81830.0171-0.15090.28790.0482-0.0024-0.0485-0.21120.0778-0.0147-0.1733-0.0087-0.02790.00060.0048-0.270713.730529.85921.6655
22.03660.9304-0.39344.8352-0.91610.1990.03040.13910.46830.00780.05020.3015-0.0969-0.0297-0.0806-0.13470.02370.00210.00170.038-0.2531-2.639832.93017.507
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 2806 - 283
2X-RAY DIFFRACTION2BB3 - 2806 - 283

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