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- PDB-1hfb: Crystal structure of the tyrosine-regulated 3-deoxy-D-arabino-hep... -

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Basic information

Entry
Database: PDB / ID: 1hfb
TitleCrystal structure of the tyrosine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Saccharomyces cerevisiae complexed with phosphoenolpyruvate
ComponentsTYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
KeywordsLYASE / BETA-ALPHA-BARREL
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 / nucleus / 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
PHOSPHOENOLPYRUVATE / Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchneider, T.R. / Hartmann, M. / Braus, G.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Evolution of Feedback-Inhibited Beta /Alpha Barrel Isoenzymes by Gene Duplication and a Single Mutation
Authors: Hartmann, M. / Schneider, T.R. / Pfeil, A. / Heinrich, G. / Lipscomb, W. / Braus, G.H.
History
DepositionNov 30, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS AB, BA, CB, DA, EB, FA, GB, AND HA BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS AB, BA, CB, DA, EB, FA, GB, AND HA BELOW ARE ACTUALLY 8-STRANDED BARRELS. THESE ARE REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
B: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
C: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
D: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
E: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
F: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
G: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
H: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,72116
Polymers318,3768
Non-polymers1,3448
Water22,5371251
1
A: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
B: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9304
Polymers79,5942
Non-polymers3362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-38.9 kcal/mol
Surface area28540 Å2
MethodPQS
2
C: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
D: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9304
Polymers79,5942
Non-polymers3362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-26.5 kcal/mol
Surface area29250 Å2
MethodPQS
3
E: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
F: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9304
Polymers79,5942
Non-polymers3362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-54.2 kcal/mol
Surface area28520 Å2
MethodPQS
4
G: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
H: TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9304
Polymers79,5942
Non-polymers3362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-37.6 kcal/mol
Surface area28870 Å2
MethodPQS
Unit cell
Length a, b, c (Å)82.000, 93.800, 104.500
Angle α, β, γ (deg.)65.60, 85.60, 75.40
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))
DetailsTHE 8 MOLECULES CONTAINED IN THE ASSYMETRIC UNIT AREARRANGED IN TWO TETRAMERS (DIMER OF DIMERS) WITH APPROXIMATE222 POINT SYMMETRY. THE TETRAMERS HAVE VERY SIMILAR ORIENTATIONS,WITH THEIR CENTERS OF MASS BEING RELATED BY ACRYSTALLOGRAPHIC TRANSLATION OF (0.5,0.5,0).

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Components

#1: Protein
TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE / PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE / DAHP SYNTHETASE / 3-DEOXY-D-ARABINO-HEPTULOSONATE 7- ...PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE / DAHP SYNTHETASE / 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE / PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE TYROSINE-INHIBITED / PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE


Mass: 39797.055 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: RH1326 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): RH1326 / References: UniProt: P32449, EC: 4.1.2.15
#2: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H5O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1251 / 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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growpH: 9 / Details: pH 9.00
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 %PEG30001reservoir
21 mMdithiothreitol1reservoirpH9.0
310 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 210365 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 2.01 % / Rmerge(I) obs: 0.037
Reflection
*PLUS
Redundancy: 2.9 % / Num. measured all: 423490
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / % possible obs: 89.3 % / Redundancy: 1.2 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAINS A AND B OF PDB ENTRY 1QR7

1qr7


Resolution: 1.9→40 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 9891 4.6 %THIN SHELLS
Rwork0.2079 ---
obs0.2079 198354 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9802 Å2 / ksol: 0.34361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.75 Å23.627 Å21.667 Å2
2---1.712 Å2-6.502 Å2
3---7.463 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20624 0 80 1251 21955
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0061
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.30021
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.66387
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78448
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.053
X-RAY DIFFRACTIONc_mcangle_it3.3884
X-RAY DIFFRACTIONc_scbond_it2.964
X-RAY DIFFRACTIONc_scangle_it4.6135
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PEP1.PARWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMPEP1.TOP
Refinement
*PLUS
Rfactor Rfree: 0.261 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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