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- PDB-9j7h: Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate ... -

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Basic information

Entry
Database: PDB / ID: 9j7h
TitleCrystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Providencia alcalifaciens complexed with quinic acid
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / DAHP Synthase / barrel domain / inhibitor / quinic acid
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
Similarity search - Function
DAHP synthase, class 1 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-QIC / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesProvidencia alcalifaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.68 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)155,8178
Polymers155,0484
Non-polymers7694
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-44 kcal/mol
Surface area43320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.978, 51.823, 133.303
Angle α, β, γ (deg.)90.00, 108.93, 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-QIC / (1S,3R,4S,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid / Quinic acid


Mass: 192.167 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25%w/v PEG3350, 0.2M Magnesium chloride, 0.1M bis Tris PH-5.5, 20% ETG

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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: Nov 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.68→25.21 Å / Num. obs: 43906 / % possible obs: 96.8 % / Redundancy: 3.5 % / CC1/2: 0.943 / Net I/σ(I): 4.5
Reflection shellResolution: 2.68→2.78 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4373 / CC1/2: 0.699 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KFL

1kfl


Resolution: 2.68→25.21 Å / Cor.coef. Fo:Fc: 0.845 / Cor.coef. Fo:Fc free: 0.787 / SU B: 32.288 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R: 1.005 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30539 2152 4.9 %RANDOM
Rwork0.26468 ---
obs0.2667 41750 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.944 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0 Å20.08 Å2
2---1.42 Å2-0 Å2
3---0.81 Å2
Refinement stepCycle: 1 / Resolution: 2.68→25.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9148 0 52 22 9222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0129341
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169043
X-RAY DIFFRACTIONr_angle_refined_deg2.5491.81812641
X-RAY DIFFRACTIONr_angle_other_deg0.8261.77220823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10751166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.415568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.581101650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.21480
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210923
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022013
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1662.3174712
X-RAY DIFFRACTIONr_mcbond_other5.1662.3174712
X-RAY DIFFRACTIONr_mcangle_it7.7664.1295862
X-RAY DIFFRACTIONr_mcangle_other7.7664.135863
X-RAY DIFFRACTIONr_scbond_it5.8822.6764629
X-RAY DIFFRACTIONr_scbond_other5.8822.6764630
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9114.7416780
X-RAY DIFFRACTIONr_long_range_B_refined11.33321.6410294
X-RAY DIFFRACTIONr_long_range_B_other11.33321.6410295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.749 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 153 -
Rwork0.323 3076 -
obs--97.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.28640.0190.1380.2506-0.06240.0898-0.01450.0206-0.0006-0.01830.02670.0309-0.01240.023-0.01210.0813-0.00890.02750.2201-0.00610.015240.8821.032914.4156
20.29750.0608-0.05570.2189-0.12850.1158-0.0198-0.0261-0.0060.0030.02780.0215-0.019-0.0039-0.0080.0780.00540.02680.2251-0.00010.013832.6207-21.999239.0071
30.22210.19290.01450.2036-0.07170.51130.0445-0.0581-0.03060.0249-0-0.0327-0.02730.0856-0.04450.036-0.02740.01150.3067-0.02590.017879.7823-10.671859.6424
40.4355-0.1902-0.05390.1699-0.09810.31340.0146-0.01290.0792-0.0223-0.03-0.02370.09770.15010.01540.04930.0380.02510.31360.00440.028990.1694-10.352927.0954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 401
2X-RAY DIFFRACTION2B2 - 402
3X-RAY DIFFRACTION3C3 - 401
4X-RAY DIFFRACTION4D3 - 401

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