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- PDB-7dlh: Crystallization of Cationic Peroxidase from Proso Millet and Iden... -

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Basic information

Entry
Database: PDB / ID: 7dlh
TitleCrystallization of Cationic Peroxidase from Proso Millet and Identification of Its Phosphatase Active Sites
Componentsperoxidase
KeywordsOXIDOREDUCTASE / Proso millet peroxidase
Function / homologyalpha-L-fucopyranose / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesPanicum miliaceum (proso millet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.789 Å
AuthorsCui, x.d. / Wang, t.f. / Wang, k.
CitationJournal: To Be Published
Title: Crystallization of Cationic Peroxidase from Proso Millet and Identification of Its Phosphatase Active Sites
Authors: Cui, x.d. / Wang, t.f.
History
DepositionNov 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,34811
Polymers36,2951
Non-polymers2,05310
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.298, 112.665, 111.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-408-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein peroxidase


Mass: 36295.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Panicum miliaceum (proso millet) / Production host: Panicum miliaceum (proso millet)

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Sugars , 3 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(2-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy- ...alpha-D-mannopyranose-(2-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa2-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+2)][D-1-deoxy-Manp]{}[(4+1)][b-D-4-deoxy-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 369 molecules

#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 mol/L Tris-HCl, pH 8.0, 0.2 mol/L MgCl2, and 25%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.789→50 Å / Num. obs: 33291 / % possible obs: 98.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.078 / Rrim(I) all: 0.16 / Χ2: 0.51 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.833.70.48616070.8350.2770.5610.44496.3
1.83-1.863.70.44716630.8620.2530.5160.45399.3
1.86-1.93.70.4516200.8510.2540.5190.48198.2
1.9-1.943.70.49516570.7390.2780.570.53799
1.94-1.983.80.37216390.8670.2110.4290.47298.4
1.98-2.033.60.28616470.9290.1650.3320.44298.4
2.03-2.083.40.27916220.8980.1670.3270.5697.5
2.08-2.133.80.24416560.9430.1360.280.48199.2
2.13-2.23.80.21116660.960.1170.2420.46498.9
2.2-2.273.80.28116500.8670.1540.3220.62398.9
2.27-2.353.70.19116780.9660.1080.220.46599.7
2.35-2.443.60.15316710.9680.0880.1770.48399.6
2.44-2.553.50.13416270.9710.080.1570.48297.2
2.55-2.693.80.13116780.9790.0730.1510.50699.3
2.69-2.863.80.11216890.9860.0630.1290.49199.4
2.86-3.083.70.09816840.9880.0560.1140.53699.8
3.08-3.393.60.08116670.990.0470.0940.5797.4
3.39-3.883.80.08316900.9910.0460.0950.64399.4
3.88-4.883.50.06617020.990.0380.0760.56597.5
4.88-503.60.06217780.9930.0350.0720.50597.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AOG

5aog


Resolution: 1.789→39.641 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 2000 6.01 %
Rwork0.171 31253 -
obs0.173 33253 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.1 Å2 / Biso mean: 16.1507 Å2 / Biso min: 5.43 Å2
Refinement stepCycle: final / Resolution: 1.789→39.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 129 362 2780
Biso mean--25.34 23.34 -
Num. residues----302
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.83330.25261280.2061200790
1.8333-1.88290.24571430.2017222798
1.8829-1.93830.26091410.2152220199
1.9383-2.00080.2241440.1832223999
2.0008-2.07230.20021400.1705219998
2.0723-2.15530.20341430.1611224199
2.1553-2.25340.23591440.1732224299
2.2534-2.37220.20661430.1639224499
2.3722-2.52080.19381430.1624223498
2.5208-2.71540.20541430.16892246100
2.7154-2.98860.20291480.1742291100
2.9886-3.42080.18251420.1717223398
3.4208-4.3090.17981490.1519231599
4.309-39.60.1971490.168233497

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