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- PDB-7zw7: Crystal structure of Schistosoma mansoni HDAC8 in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 7zw7
TitleCrystal structure of Schistosoma mansoni HDAC8 in complex with a formate molecule in the active site
ComponentsPutative histone deacetylase 1, 2,3
KeywordsHYDROLASE / Histone deacetylase 8 / Schistosoma mansoni / Formate
Function / homologyHistone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / FORMIC ACID / : / DI(HYDROXYETHYL)ETHER / Putative histone deacetylase 1, 2,3
Function and homology information
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsSaccoccia, F. / Giannaccari, M. / Ruberti, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Regione Lazio (Italy)A0375-2020-36575 Italy
CitationJournal: To Be Published
Title: Crystal structure of Schistosoma mansoni HDAC8 in complex with a formate molecule in the active site
Authors: Saccoccia, F. / Giannaccari, M. / Ruberti, G.
History
DepositionMay 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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: Putative histone deacetylase 1, 2,3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2118
Polymers49,8341
Non-polymers3777
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-47 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.957, 70.957, 180.514
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative histone deacetylase 1, 2,3


Mass: 49834.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3Q0KJ63

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Non-polymers , 6 types, 16 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.2M sodium formate, 0.1M bis-tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→45.89 Å / Num. obs: 11416 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 45.91 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.466 / Rpim(I) all: 0.171 / Rrim(I) all: 0.498 / Χ2: 0.99 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-38.42.319116100.3320.8412.4730.9699.9
9.01-45.896.40.09613.64220.9950.040.1050.9398.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6 Å45.89 Å
Translation6 Å45.89 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PHENIX1.19-4092refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ5

4bz5


Resolution: 2.85→45.89 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0.2 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2749 1029 5.02 %
Rwork0.2343 19450 -
obs0.2363 10831 99.62 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.51 Å2 / Biso mean: 46.1877 Å2 / Biso min: 32.08 Å2
Refinement stepCycle: final / Resolution: 2.85→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3267 0 29 9 3305
Biso mean--41.08 41.56 -
Num. residues----408
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-30.35161410.342727822923100
3-3.190.34751490.315127702919100
3.19-3.430.33291490.29927962945100
3.43-3.780.29381470.246927792926100
3.78-4.330.25511410.198227772918100
4.33-5.450.27541510.192928032954100
5.45-45.890.19391510.18942743289499
Refinement TLS params.Method: refined / Origin x: -8.614 Å / Origin y: 22.0787 Å / Origin z: 15.4252 Å
111213212223313233
T0.3855 Å20.0063 Å20.0698 Å2-0.3114 Å2-0.0038 Å2--0.3641 Å2
L1.6951 °20.0738 °2-0.1797 °2-2.4272 °20.0741 °2--2.3664 °2
S-0.0314 Å °0.0152 Å °-0.0081 Å °-0.1048 Å °0.034 Å °-0.0501 Å °-0.0129 Å °0.0641 Å °-0.0009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 435
2X-RAY DIFFRACTION1allA501 - 608
3X-RAY DIFFRACTION1allS1 - 12

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