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- PDB-7ykc: crystal structure of the Phenylalanine-regulated 3-deoxy-D-arabin... -

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Basic information

Entry
Database: PDB / ID: 7ykc
Titlecrystal structure of the Phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (ARO3) from Saccharomyces cerevisiae
Components3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
KeywordsBIOSYNTHETIC PROTEIN / DAHP synthase / ARO3
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 / mitochondrion / nucleus / cytoplasm
Similarity search - Function
DAHP synthase, class 1 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase-type TIM barrel
Similarity search - Domain/homology
Phospho-2-dehydro-3-deoxyheptonate aldolase, phenylalanine-inhibited
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLiu, H. / Luo, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0903300 China
CitationJournal: Commun Chem / Year: 2023
Title: Mechanistic investigation of a D to N mutation in DAHP synthase that dictates carbon flux into the shikimate pathway in yeast.
Authors: Liu, H. / Xiao, Q. / Wu, X. / Ma, H. / Li, J. / Guo, X. / Liu, Z. / Zhang, Y. / Luo, Y.
History
DepositionJul 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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 synthase
B: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)82,2602
Polymers82,2602
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-33 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.680, 95.561, 105.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3- ...3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3-deoxyheptonate aldolase


Mass: 41129.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: ARO3, YDR035W, YD9673.07 / Production host: Escherichia coli B (bacteria)
References: UniProt: P14843, 3-deoxy-7-phosphoheptulonate synthase

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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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, 20% v/v Polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.3→105.79 Å / Num. obs: 11363 / % possible obs: 96.6 % / Redundancy: 7 % / Biso Wilson estimate: 128.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.047 / Rrim(I) all: 0.125 / Net I/σ(I): 9.6 / Num. measured all: 79559
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.3-3.567.31.5031660422760.6230.5871.6171.395.9
8.73-105.795.90.05542217110.9960.0240.0627.998.9

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
Blu-Icedata collection
Aimlessdata scaling
PHENIXphasing
autoPROCdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 3.3→34.37 Å / SU ML: 0.75 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.295 1130 9.98 %
Rwork0.252 --
obs0.2562 11322 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5759 0 0 0 5759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135850
X-RAY DIFFRACTIONf_angle_d1.767866
X-RAY DIFFRACTIONf_dihedral_angle_d15.1322256
X-RAY DIFFRACTIONf_chiral_restr0.096866
X-RAY DIFFRACTIONf_plane_restr0.0131034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.450.49391300.39851185X-RAY DIFFRACTION93
3.45-3.630.41311430.36311289X-RAY DIFFRACTION100
3.63-3.860.3891300.34581165X-RAY DIFFRACTION89
3.86-4.160.33591310.34021191X-RAY DIFFRACTION91
4.16-4.570.33171460.28161304X-RAY DIFFRACTION100
4.57-5.230.2381460.25831318X-RAY DIFFRACTION100
5.24-6.590.30561480.26981335X-RAY DIFFRACTION100
6.59-34.370.24761560.17891402X-RAY DIFFRACTION99
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)
12.935-0.3992-1.67895.84620.7633.8043-0.47380.06180.1474-0.2336-0.36070.4731-1.89960.66340.82091.2382-0.2947-0.380.7820.29980.9287-30.1041-32.825-2.8153
21.6675-0.2042-2.31586.0307-5.49538.138-0.4894-0.41260.9320.62360.16910.9206-2.5606-0.8361-0.06561.30380.0951-0.44020.94120.00791.6541-41.6393-24.8568-3.5299
35.05751.05061.65245.9276-0.18945.5627-0.6737-0.09451.2754-1.0051-0.53520.8035-3.56280.72120.81242.8262-0.3571-0.81270.90590.32161.4596-32.1487-17.3842-8.5315
45.3887-0.65960.93654.8005-0.47985.4488-0.80342.2041-0.7095-0.8292-0.0532-0.1935-1.11221.3661.01651.1516-0.23180.01981.44410.06471.022-18.6247-38.0934-16.0567
52.99791.46330.41225.88632.14641.6919-0.00590.31180.99010.9489-0.5328-2.6566-0.44592.46260.26911.3284-0.5635-0.51662.70750.24761.9759-2.1602-29.602811.8897
64.65240.42721.87726.63852.85243.0916-0.1676-0.67581.68910.0835-0.3881-0.7135-1.56590.80440.57181.6699-0.8639-0.34021.83140.19411.4788-14.96-16.50915.1588
71.2895-2.09090.51181.9488-0.17261.42771.83850.2728-0.2024-0.1265-1.0688-1.7293-1.41481.920.00351.7924-1.0745-0.38813.17780.16743.0074.0133-15.215114.5564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 127 )
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 370 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 27 )
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 170 )
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 303 )
7X-RAY DIFFRACTION7chain 'B' and (resid 304 through 370 )

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