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- PDB-6agm: Molecular basis for feedback inhibition of tyrosine-regulated 3-d... -

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Basic information

Entry
Database: PDB / ID: 6agm
TitleMolecular basis for feedback inhibition of tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Escherichia coli
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
KeywordsBIOSYNTHETIC PROTEIN / 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) / Escherichia coli / aromatic amino acid biosynthesis / feedback inhibition / allosteric regulation.
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 / identical protein binding / cytoplasm
Similarity search - Function
DAHP synthase, class 1 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
TYROSINE / Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCui, D. / Qi, J. / Wen, T.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Molecular basis for feedback inhibition of tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Escherichia coli.
Authors: Cui, D. / Deng, A. / Bai, H. / Yang, Z. / Liang, Y. / Liu, Z. / Qiu, Q. / Wang, L. / Liu, S. / Zhang, Y. / Shi, Y. / Qi, J. / Wen, T.
History
DepositionAug 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

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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, Tyr-sensitive
B: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
C: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
D: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,8248
Polymers155,0994
Non-polymers7254
Water5,080282
1
A: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
hetero molecules

C: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9124
Polymers77,5502
Non-polymers3622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_547-x,y-1/2,-z+21
Buried area6140 Å2
ΔGint-12 kcal/mol
Surface area24020 Å2
MethodPISA
2
B: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
hetero molecules

D: Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9124
Polymers77,5502
Non-polymers3622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y+1/2,-z+31
Buried area6230 Å2
ΔGint-13 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.189, 133.859, 87.670
Angle α, β, γ (deg.)90.00, 91.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive / 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: 38774.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: aroF, b2601, JW2582 / Production host: Escherichia coli (E. coli)
References: UniProt: P00888, 3-deoxy-7-phosphoheptulonate synthase
#2: Chemical
ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 16% PEG 4000, 10% 2-propanol, 0.1 M sodium citrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 82353 / % possible obs: 97 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rpim(I) all: 0.036 / Rsym value: 0.088 / Net I/σ(I): 19.4
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 6902 / CC1/2: 0.651 / Rpim(I) all: 0.368 / Rsym value: 0.788

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QR7

1qr7


Resolution: 2→38.207 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.62
RfactorNum. reflection% reflection
Rfree0.2288 4111 5 %
Rwork0.1933 --
obs0.195 82301 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→38.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10232 0 0 282 10514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910408
X-RAY DIFFRACTIONf_angle_d0.73714104
X-RAY DIFFRACTIONf_dihedral_angle_d25.4793900
X-RAY DIFFRACTIONf_chiral_restr0.0441588
X-RAY DIFFRACTIONf_plane_restr0.0051880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9937-2.01720.3577950.29952053X-RAY DIFFRACTION74
2.0172-2.04180.3241130.28872300X-RAY DIFFRACTION82
2.0418-2.06760.29631170.27752382X-RAY DIFFRACTION86
2.0676-2.09480.32151340.27362494X-RAY DIFFRACTION89
2.0948-2.12350.29261480.27312537X-RAY DIFFRACTION92
2.1235-2.15390.33231610.27692590X-RAY DIFFRACTION95
2.1539-2.1860.31091230.26272697X-RAY DIFFRACTION97
2.186-2.22020.26511490.25032712X-RAY DIFFRACTION98
2.2202-2.25660.2791390.2422796X-RAY DIFFRACTION99
2.2566-2.29550.2591450.2422736X-RAY DIFFRACTION100
2.2955-2.33720.3021280.23832779X-RAY DIFFRACTION100
2.3372-2.38220.26211250.23262800X-RAY DIFFRACTION100
2.3822-2.43080.24681530.22922790X-RAY DIFFRACTION100
2.4308-2.48360.30111670.23322734X-RAY DIFFRACTION100
2.4836-2.54140.29821640.22632755X-RAY DIFFRACTION100
2.5414-2.60490.26691630.22872786X-RAY DIFFRACTION100
2.6049-2.67530.25431390.22712767X-RAY DIFFRACTION100
2.6753-2.7540.26291460.22542765X-RAY DIFFRACTION100
2.754-2.84290.2411480.2332804X-RAY DIFFRACTION100
2.8429-2.94450.27311470.23352747X-RAY DIFFRACTION100
2.9445-3.06230.24971300.22562818X-RAY DIFFRACTION100
3.0623-3.20160.26881310.21892808X-RAY DIFFRACTION100
3.2016-3.37030.25511520.20642777X-RAY DIFFRACTION100
3.3703-3.58130.23521500.1872768X-RAY DIFFRACTION100
3.5813-3.85760.21881580.17962766X-RAY DIFFRACTION100
3.8576-4.24540.20521560.15382782X-RAY DIFFRACTION100
4.2454-4.85860.16661510.152807X-RAY DIFFRACTION100
4.8586-6.11730.2071380.17012798X-RAY DIFFRACTION100
6.1173-38.2140.16651410.15052842X-RAY DIFFRACTION100
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.71330.0898-0.25790.82250.16980.74420.03160.05560.1238-0.0872-0.0110.0596-0.0412-0.02470.271-0.0059-0.02160.2519-0.00530.25651.328617.7391102.7374
21.54470.3719-0.0950.6576-0.06770.94670.035-0.03060.070.09320.02170.06410.0864-0.08780.35020.02260.01550.3380.0130.3378-25.26355.7904119.2073
31.0755-0.33690.17671.9543-0.30920.89940.02690.0417-0.0669-0.1441-0.0116-0.04890.0986-0.01450.2992-0.00290.02230.2949-0.00330.3088-18.999253.150674.6699
40.75070.36210.09791.2887-0.25550.6112-0.02810.03410.04230.15820.0421-0.0129-0.1585-0.04190.38970.0326-0.00630.37830.00220.33425.942720.3068147.6963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 350 )
2X-RAY DIFFRACTION2chain 'B' and (resid 10 through 350 )
3X-RAY DIFFRACTION3chain 'C' and (resid 10 through 350 )
4X-RAY DIFFRACTION4chain 'D' and (resid 10 through 350 )

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