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- PDB-1qr7: CRYSTAL STRUCTURE OF PHENYLALANINE-REGULATED 3-DEOXY-D-ARABINO-HE... -

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Basic information

Entry
Database: PDB / ID: 1qr7
TitleCRYSTAL STRUCTURE OF PHENYLALANINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM ESCHERICHIA COLI COMPLEXED WITH PB2+ AND PEP
ComponentsPHENYLALANINE-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 / identical protein binding / cytosol / 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
LEAD (II) ION / PHOSPHOENOLPYRUVATE / Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsShumilin, I.A. / Kretsinger, R.H. / Bauerle, R.H.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli.
Authors: Shumilin, I.A. / Kretsinger, R.H. / Bauerle, R.H.
#1: Journal: Proteins / Year: 1996
Title: Purification, crystallization, and preliminary crystallographic analysis of 3- deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli
Authors: Shumilin, I.A. / Kretsinger, R.H. / Bauerle, R.H.
History
DepositionJun 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHENYLALANINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
B: PHENYLALANINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
C: PHENYLALANINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
D: PHENYLALANINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,12316
Polymers152,2384
Non-polymers1,88512
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16280 Å2
ΔGint-115 kcal/mol
Surface area44470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.731, 51.326, 148.099
Angle α, β, γ (deg.)90.00, 116.43, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsThe biological assembly is a tetramer that consists of the chains A, B, C, and D related by 222 symmetry

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Components

#1: Protein
PHENYLALANINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE / E.C. 4.1.2.15 / PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE / DAHP SYNTHETASE


Mass: 38059.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AB91, EC: 4.1.2.15
#2: Chemical
ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pb
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 168.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: PEG 1000, ethanol, lithium sulphate, bis-tris propane pH 8.8, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal grow
*PLUS
pH: 8.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.8 mg/mlprotein1drop
21.63 mMPEP1drop
30.4 mM1dropPb(CH3COO)2
40.1 M1dropLi2SO4
512 %(w/v)PEG10001drop
650 mMBTP1drop
719 %(w/v)PEG10001reservoir
80.1 M1reservoirLiSO4
920 %(v/v)ethanol1reservoir
1050 mMBTP1reservoir

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.93892
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93892 Å / Relative weight: 1
ReflectionResolution: 2.6→18 Å / Num. all: 40409 / Num. obs: 40392 / % possible obs: 91.8 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.118 / Num. unique all: 2825 / % possible all: 64.6
Reflection shell
*PLUS
% possible obs: 64.6 % / Mean I/σ(I) obs: 8.5

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Processing

Software
NameVersionClassification
MLPHAREphasing
DMmodel building
SHELXSphasing
REFMACrefinement
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(TRUNCATE)data scaling
DMphasing
RefinementResolution: 2.6→18 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3954 9.8 %thin shells
Rwork0.194 ---
all-40409 --
obs-40259 --
Refinement stepCycle: LAST / Resolution: 2.6→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10291 0 64 4 10359
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d2.8
X-RAY DIFFRACTIONp_bond_d0.016
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / σ(F): 2 / % reflection Rfree: 9.8 % / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d2.8

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