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- PDB-7xkc: Crystal structure of Daucus Carrot hypoglycemic peptide (DCHP) -

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Basic information

Entry
Database: PDB / ID: 7xkc
TitleCrystal structure of Daucus Carrot hypoglycemic peptide (DCHP)
ComponentsDCHP
KeywordsPLANT PROTEIN / Daucus Carrot / hypoglycemic peptide / a-glycosidase inhibitor.
Function / homologyProteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / serine-type endopeptidase inhibitor activity / response to wounding / Uncharacterized protein
Function and homology information
Biological speciesDaucus carota subsp. sativus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsGuo, T. / Ren, J.Q. / Wang, L. / Shi, Y.W. / Feng, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800656 China
National Natural Science Foundation of China (NSFC)32071191 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Characterization of a thermostable, protease-tolerant inhibitor of alpha-glycosidase from carrot: A potential oral additive for treatment of diabetes.
Authors: Hao, Y. / Guo, T. / Ren, J. / Wang, Y. / Wang, L. / Shi, Y. / Feng, W.
History
DepositionApr 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DCHP
B: DCHP
C: DCHP
D: DCHP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9667
Polymers40,6784
Non-polymers2883
Water75742
1
A: DCHP


Theoretical massNumber of molelcules
Total (without water)10,1691
Polymers10,1691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5570 Å2
MethodPISA
2
B: DCHP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2662
Polymers10,1691
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area5420 Å2
MethodPISA
3
C: DCHP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2662
Polymers10,1691
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area5670 Å2
MethodPISA
4
D: DCHP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2662
Polymers10,1691
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area5810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.850, 66.210, 121.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
DCHP


Mass: 10169.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Daucus carota subsp. sativus (plant) / Gene: DCAR_011990
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A166C3G6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium sulfate decahydrate, 20% (w/v) Polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.56→44.78 Å / Num. obs: 14451 / % possible obs: 99.1 % / Redundancy: 9.5 % / CC1/2: 0.975 / Rmerge(I) obs: 0.2 / Net I/σ(I): 14.8
Reflection shellResolution: 2.56→2.63 Å / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 955 / CC1/2: 0.597 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rdy

3rdy


Resolution: 2.56→44.78 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2899 1438 10 %
Rwork0.2415 12947 -
obs0.2463 14385 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.22 Å2 / Biso mean: 60.2293 Å2 / Biso min: 34.9 Å2
Refinement stepCycle: final / Resolution: 2.56→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 15 42 2586
Biso mean--74.58 53.52 -
Num. residues----331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.56-2.650.30811320.29771179131192
2.65-2.760.32171400.29091262140299
2.76-2.880.33651420.28821275141799
2.88-3.040.35681440.278412911435100
3.04-3.230.28631430.248512931436100
3.23-3.470.27771430.237312881431100
3.47-3.820.26251450.23891311145699
3.82-4.370.27661470.21421308145599
4.38-5.510.28011490.221113461495100
5.51-44.780.29871530.24671394154799
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)
10.56610.822-0.08332.06130.91774.00910.1876-0.12790.0208-0.0742-0.09030.0797-0.19280.1528-0.09730.2173-0.0279-0.02070.27140.02790.016636.27255.58250.273
22.27961.02491.58912.66921.91936.01910.0012-0.0223-0.1649-0.23830.0848-0.15780.0726-0.2297-0.0860.1551-0.00320.0350.1857-0.00040.020725.38237.93141.049
32.02950.2453-1.08721.5951-0.98076.22110.196-0.11190.016-0.0139-0.07910.0841-0.21120.27-0.11690.1344-0.05930.01370.232-0.0490.013730.83158.43873.859
41.15370.3185-0.4663.3854-0.56385.71130.0205-0.40840.0663-0.46050.098-0.128-0.39670.1325-0.11850.4414-0.09340.06010.1675-0.03760.015122.31743.35917.062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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