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- PDB-1ofo: Crystal Structure of the Tyrosine Regulated 3-Deoxy-D-Arabino-Hep... -

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Basic information

Entry
Database: PDB / ID: 1ofo
TitleCrystal Structure of the Tyrosine Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase from Saccharomyces Cerevisiae in Complex with 2-Phosphoglycolate
ComponentsPHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
KeywordsLYASE / BETA-ALPHA-BARREL / AROMATIC AMINO-ACID BIOSYNTHESIS SYNTHASE / ALDOLASE / SYNTHETASE / MANGANESE
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
2-PHOSPHOGLYCOLIC ACID / Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsKoenig, V. / Pfeil, A. / Heinrich, G. / Braus, G. / 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. / Heinrich, G. / Braus, G. / 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 1.3May 30, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
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
Revision 2.0May 1, 2024Group: Atomic model / Category: atom_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
B: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9064
Polymers79,5942
Non-polymers3122
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)196.457, 50.955, 64.976
Angle α, β, γ (deg.)90.00, 106.41, 90.00
Int Tables number5
Space group name H-MC121

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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.: 2
Source method: isolated from a genetically manipulated source
Details: 2-PHOSPHOGLYCOLATE
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: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ROTATING ANODE (CU) / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2001 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→17.3 Å / Num. obs: 198507 / % possible obs: 95.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.0444 / Net I/σ(I): 19.77
Reflection shellResolution: 1.86→1.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.3035 / Mean I/σ(I) obs: 4.36 / % possible all: 89.1

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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 (MOLECULE A)

1hfb


Resolution: 1.86→17.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2493 5 %RANDOM
Rwork0.165 ---
obs-47358 95.6 %-
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: 25.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.86→17.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5165 0 18 403 5586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215256
X-RAY DIFFRACTIONr_bond_other_d00.024823
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.9587114
X-RAY DIFFRACTIONr_angle_other_deg3.705311236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085679
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_restr0.1360.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025884
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02978
X-RAY DIFFRACTIONr_nbd_refined0.2270.21081
X-RAY DIFFRACTIONr_nbd_other0.2920.25319
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1080.22463
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0471.53373
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87125414
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.11431883
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0154.51700
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: 1.86→1.91 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 156
Rwork0.233 3093

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