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- PDB-1ofp: CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEP... -

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Basic information

Entry
Database: PDB / ID: 1ofp
TitleCRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE
ComponentsPHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
KeywordsLYASE / BETA-ALPHA-BARREL / AROMATIC AMINO-ACID BIOSYNTHESIS
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
Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKoenig, V. / Pfeil, A. / Heinrich, G. / Braus, G.H. / Schneider, T.R.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Substrate and Metal Complexes of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase from Saccharomyces Cerevisiae Provide New Insights Into the Catalytic Mechanism
Authors: Koenig, V. / Pfeil, A. / Braus, G.H. / Schneider, T.R.
#1: Journal: 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. / Pfeil, A. / Heinrich, G. / Lipscomb, W. / Braus, G.
History
DepositionApr 17, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2004Provider: 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-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: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
B: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
C: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
D: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE


Theoretical massNumber of molelcules
Total (without water)159,1884
Polymers159,1884
Non-polymers00
Water1,856103
1
A: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
B: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE


Theoretical massNumber of molelcules
Total (without water)79,5942
Polymers79,5942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
D: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE


Theoretical massNumber of molelcules
Total (without water)79,5942
Polymers79,5942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.590, 69.004, 102.450
Angle α, β, γ (deg.)106.38, 101.48, 94.81
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE / 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


Mass: 39797.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: METAL AND COMPOUND FREE
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: RH1326 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P32449, EC: 4.1.2.15
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: 2-DEHYDRO-3-DEOXY-D-ARABINO-HEPTONATE 7- PHOSPHATE + PHOSPHATE = ...CATALYTIC ACTIVITY: 2-DEHYDRO-3-DEOXY-D-ARABINO-HEPTONATE 7- PHOSPHATE + PHOSPHATE = PHOSPHOENOLPYRUVATE + D-ERYTHROSE 4- PHOSPHATE + 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growpH: 8
Details: TRIS PH 7.5-9.0 10 MM 20% PEG3400, 13-17MG/ML DAHPS

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9094
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9094 Å / Relative weight: 1
ReflectionResolution: 2→19.9 Å / Num. obs: 414373 / % possible obs: 97.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.1
Reflection shellResolution: 2.03→2.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3.3 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HFB

1hfb


Resolution: 2.1→19.88 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.576 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3800 5 %RANDOM
Rwork0.205 ---
obs-71709 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 46.27 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9225 0 0 103 9328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0430.0219356
X-RAY DIFFRACTIONr_bond_other_d0.0020.028712
X-RAY DIFFRACTIONr_angle_refined_deg2.8641.94712706
X-RAY DIFFRACTIONr_angle_other_deg1.25320148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.53251234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1980.21536
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0210548
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021779
X-RAY DIFFRACTIONr_nbd_refined0.2380.21965
X-RAY DIFFRACTIONr_nbd_other0.260.210003
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.110.25895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4090.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3780.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8991.56222
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.15329889
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.76933134
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.2784.52817
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 285
Rwork0.252 5218

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