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- PDB-9j7s: Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate ... -

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Basic information

Entry
Database: PDB / ID: 9j7s
TitleCrystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Providencia alcalifaciens complexed with Phe
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / DAHP Synthase / inhibitor / barrel domain
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 / cytoplasm
Similarity search - Function
DAHP synthase, class 1 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase-type TIM barrel
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHENYLALANINE / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesProvidencia alcalifaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJangid, K. / Mahto, J.K. / Kumar, K.A. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Arch.Biochem.Biophys. / Year: 2025
Title: Structural and biochemical analyses reveal quinic acid inhibits DAHP synthase a key player in shikimate pathway.
Authors: Jangid, K. / Mahto, J.K. / Kumar, K.A. / Dhaka, P. / Sharma, A. / Tariq, A. / Sharma, A.K. / Kumar, P.
History
DepositionAug 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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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
C: Phospho-2-dehydro-3-deoxyheptonate aldolase
D: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,8159
Polymers155,0484
Non-polymers7675
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13230 Å2
ΔGint-41 kcal/mol
Surface area43440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.234, 51.468, 132.657
Angle α, β, γ (deg.)90.00, 113.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phospho-2-dehydro-3-deoxyheptonate aldolase


Mass: 38761.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Providencia alcalifaciens (bacteria) / Gene: PROVALCAL_03276 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B6XIT1, 3-deoxy-7-phosphoheptulonate synthase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 16% PEG3350, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, and 2% v/v Tacsimate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.5→25.17 Å / Num. obs: 53799 / % possible obs: 99.8 % / Redundancy: 7.7 % / CC1/2: 0.978 / Net I/σ(I): 6.8
Reflection shellResolution: 2.5→2.58 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5370 / CC1/2: 0.736

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KFL

1kfl


Resolution: 2.5→25.17 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.863 / SU B: 0.007 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 2711 5 %RANDOM
Rwork0.23425 ---
obs0.23583 51076 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.025 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20.17 Å2
2--1.28 Å20 Å2
3----1.63 Å2
Refinement stepCycle: 1 / Resolution: 2.5→25.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9280 0 55 35 9370
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 195 -
Rwork0.298 3725 -
obs--100 %

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