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- PDB-8ql0: Structure of human PAD6 Phosphomimic mutant V10E/S446E, apo -

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Basic information

Entry
Database: PDB / ID: 8ql0
TitleStructure of human PAD6 Phosphomimic mutant V10E/S446E, apo
ComponentsProtein-arginine deiminase type-6
KeywordsUNKNOWN FUNCTION / peptidylarginine deiminase / apo / mammalian fertilization / cytoplasmic lattice
Function / homology
Function and homology information


regulation of translation by machinery localization / cytoplasm organization / protein-arginine deiminase / cortical granule / protein-arginine deiminase activity / embryonic cleavage / intermediate filament cytoskeleton / Chromatin modifying enzymes / cytoskeleton organization / calcium ion binding ...regulation of translation by machinery localization / cytoplasm organization / protein-arginine deiminase / cortical granule / protein-arginine deiminase activity / embryonic cleavage / intermediate filament cytoskeleton / Chromatin modifying enzymes / cytoskeleton organization / calcium ion binding / nucleus / cytoplasm
Similarity search - Function
Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / Cupredoxin
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Protein-arginine deiminase type-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.675 Å
AuthorsRanaivoson, F.M. / Beaumont, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-035107 United States
CitationJournal: Iucrj / Year: 2024
Title: Crystal structure of human peptidylarginine deiminase type VI (PAD6) provides insights into its inactivity.
Authors: Ranaivoson, F.M. / Bande, R. / Cardaun, I. / De Riso, A. / Gartner, A. / Loke, P. / Reinisch, C. / Vogirala, P. / Beaumont, E.
History
DepositionSep 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-arginine deiminase type-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5498
Polymers77,7591
Non-polymers7907
Water5,477304
1
A: Protein-arginine deiminase type-6
hetero molecules

A: Protein-arginine deiminase type-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,09916
Polymers155,5182
Non-polymers1,58114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8820 Å2
ΔGint-14 kcal/mol
Surface area51270 Å2
Unit cell
Length a, b, c (Å)127.323, 54.318, 106.785
Angle α, β, γ (deg.)90.00, 108.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein-arginine deiminase type-6 / Peptidyl arginine deiminase-like protein / Peptidylarginine deiminase VI / hPADVI / Protein- ...Peptidyl arginine deiminase-like protein / Peptidylarginine deiminase VI / hPADVI / Protein-arginine deiminase type VI


Mass: 77759.023 Da / Num. of mol.: 1 / Mutation: S10E, S446E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI6, PAD6 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q6TGC4, protein-arginine deiminase

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Non-polymers , 5 types, 311 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 15-18 % PEG 3350, 200-300 mM NaBr, 0.1 M bis-tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.675→101.2 Å / Num. obs: 41323 / % possible obs: 78.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 13.6
Reflection shellResolution: 1.675→1.851 Å / Num. unique obs: 2067 / CC1/2: 0.776

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (22-FEB-2023)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.675→101.2 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.22 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.182
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 2087 5.05 %RANDOM
Rwork0.1965 ---
obs0.1987 41323 51.8 %-
Displacement parametersBiso mean: 35.13 Å2
Baniso -1Baniso -2Baniso -3
1--2.4603 Å20 Å20.3965 Å2
2--6.6265 Å20 Å2
3----4.1662 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.675→101.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5049 0 51 304 5404
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015298HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.017177HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1853SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes875HARMONIC5
X-RAY DIFFRACTIONt_it5298HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion16.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion685SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4548SEMIHARMONIC4
LS refinement shellResolution: 1.68→1.78 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2757 -6.29 %
Rwork0.2617 775 -
all0.2627 827 -
obs--6.3 %
Refinement TLS params.Method: refined / Origin x: 12.7996 Å / Origin y: 2.3951 Å / Origin z: 9.329 Å
111213212223313233
T-0.0695 Å2-0.0189 Å20.0012 Å2-0.0855 Å2-0.011 Å2---0.0772 Å2
L0.2367 °2-0.0915 °2-0.3163 °2-0.0454 °20.3105 °2--1.5171 °2
S0.0405 Å °-0.0198 Å °0.0233 Å °-0.0174 Å °0.0064 Å °-0.0051 Å °-0.0306 Å °0.1397 Å °-0.0469 Å °
Refinement TLS groupSelection details: { A|* }

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