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- PDB-1kfl: Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-he... -

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Basic information

Entry
Database: PDB / ID: 1kfl
TitleCrystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from E.coli complexed with Mn2+, PEP, and Phe
Components3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
KeywordsLYASE / beta/alpha barrel / allosteric inhibition / feedback regulation / aromatic biosynthetic pathway
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 / cytosol
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 / PHENYLALANINE / Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive / Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsShumilin, I.A. / Zhao, C. / Bauerle, R. / Kretsinger, R.H.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Allosteric inhibition of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase alters the coordination of both substrates.
Authors: Shumilin, I.A. / Zhao, C. / Bauerle, R. / Kretsinger, R.H.
History
DepositionNov 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
C: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
D: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
E: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
F: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
G: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
H: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,12048
Polymers307,4778
Non-polymers4,64240
Water00
1
A: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
B: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
C: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
D: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,06024
Polymers153,7394
Non-polymers2,32120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19930 Å2
ΔGint-216 kcal/mol
Surface area45670 Å2
MethodPISA
2
E: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
F: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
G: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
H: 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,06024
Polymers153,7394
Non-polymers2,32120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20030 Å2
ΔGint-221 kcal/mol
Surface area45470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)290.097, 90.097, 155.798
Angle α, β, γ (deg.)90.00, 120.77, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsThe biological assembly is a tetramer, two tetramers, ABCD and EFGH, reside in the asymmetric unit.

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Components

#1: Protein
3-deoxy-D-arabino-heptulosonate-7-phosphate synthase / E.C.4.1.2.15 / PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE / PHE-SENSITIVE / DAHP synthetase / phenylalanine ...PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE / PHE-SENSITIVE / DAHP synthetase / phenylalanine repressible / PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE


Mass: 38434.660 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aroG / Plasmid: pTTG6 / Production host: Escherichia coli (E. coli) / Strain (production host): CB650
References: UniProt: P00886, UniProt: P0AB91*PLUS, EC: 4.1.2.15
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H5O6P
Has protein modificationY

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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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: PEG 4000, lithium sulfate, manganese sulfate, phosphoenolpyruvate, phenylalanine, bis-tris-propane, pH 8.1, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal
*PLUS
Density % sol: 58 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112.0 mg/mlDAHPS1drop
23.3 mMPhe1drop
33.3 mMPEP1drop
41.7 mM1dropMnSO4
50.1 M1dropLi2SO4
612 %(w/v)PEG40001reservoir
750 mMbis-Tris-propane1reservoirpH8.1

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97165 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 2000 / Details: mirrors
RadiationMonochromator: Sagitally focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97165 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 84564 / Num. obs: 84546 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 24
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 5.3 / % possible all: 98.7
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 84564 / % possible obs: 99.4 % / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.313

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Processing

Software
NameVersionClassification
MLPHAREphasing
DMmodel building
CNSrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(TRUNCATE)data scaling
DMphasing
CNSphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1QR7

1qr7


Resolution: 2.8→20 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2598 3.1 %random
Rwork0.218 ---
all0.219 84546 --
obs0.219 84545 100 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.34 Å20 Å2-5.4 Å2
2---11.657 Å20 Å2
3---8.317 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21411 0 264 0 21675
Refinement
*PLUS
% reflection Rfree: 3 % / Rfactor all: 0.219 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.3

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