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- PDB-1n8f: Crystal structure of E24Q mutant of phenylalanine-regulated 3-deo... -

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Basic information

Entry
Database: PDB / ID: 1n8f
TitleCrystal structure of E24Q mutant of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Escherichia Coli in complex with Mn2+ and PEP
ComponentsDAHP Synthetase
KeywordsMETAL BINDING PROTEIN / (Beta/Alpha)8 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
: / PHOSPHOENOLPYRUVATE / Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsShumilin, I.A. / Bauerle, R. / Kretsinger, R.H.
CitationJournal: Biochemistry / Year: 2003
Title: The High-Resolution Structure of 3-Deoxy-D-arabino-heptulosonate-7-phosphate Synthase Reveals a Twist in the Plane of Bound Phosphoenolpyruvate
Authors: Shumilin, I.A. / Bauerle, R. / Kretsinger, R.H.
History
DepositionNov 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_asym_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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DAHP Synthetase
B: DAHP Synthetase
C: DAHP Synthetase
D: DAHP Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,89520
Polymers152,2344
Non-polymers1,66016
Water25,1311395
1
A: DAHP Synthetase
B: DAHP Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,94710
Polymers76,1172
Non-polymers8308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-82 kcal/mol
Surface area24720 Å2
MethodPISA
2
C: DAHP Synthetase
D: DAHP Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,94710
Polymers76,1172
Non-polymers8308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-84 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.224, 53.277, 150.245
Angle α, β, γ (deg.)90.00, 116.90, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly of the wild type DAHP synthase is a tetramer similar to the one located in the asymmetric unit of E24Q mutant.

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Components

#1: Protein
DAHP Synthetase / 2-dehydro-3-deoxyphosphoheptonate aldolase


Mass: 38058.520 Da / Num. of mol.: 4 / Mutation: E24Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AroG / Plasmid: pTAG29 / Production host: Escherichia coli (E. coli) / Strain (production host): CB961 / References: UniProt: P0AB91, EC: 4.1.2.15
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / 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.: 1395 / 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: 2.28 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: PEG4000, manganese sulfate, phosphoenolpyruvate, lithium sulfate, bis-tris propane, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
17 mg/mlprotein1drop
24.2 mMPEP1drop
30.7 mM1dropMnSO4
40.1 M1dropLi2SO4
512 %(w/v)PEG40001drop
650 mMBTP1droppH8.1
730 %PEG40001reservoir
80.1 M1reservoirLi2SO4
920 %(v/v)ethanol1reservoir
1050 mMBTP1reservoirpH8.1

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 19, 2001 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 152257 / Num. obs: 151346 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.5
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.5 / % possible all: 98.6
Reflection shell
*PLUS
% possible obs: 98.6 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
TRUNCATEdata reduction
CNSrefinement
ARPmodel building
HKL-2000data scaling
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3033 -random
Rwork0.209 ---
all-151346 --
obs-151346 99.4 %-
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.22 Å20 Å2-3.63 Å2
2--13.1 Å20 Å2
3----8.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10455 0 84 1395 11934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d22
X-RAY DIFFRACTIONx_improper_angle_d0.85
Refinement
*PLUS
% reflection Rfree: 2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.85

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