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- PDB-9fmn: Structure of Human PADI6 -

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Basic information

Entry
Database: PDB / ID: 9fmn
TitleStructure of Human PADI6
ComponentsProtein-arginine deiminase type-6
KeywordsHYDROLASE / DEIMINASE / PADI6
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
Protein-arginine deiminase type-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsMouilleron, S. / Walport, L. / Williams, J. / Marsh, A.J. / Hernandez Trapero, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Comput Struct Biotechnol J / Year: 2024
Title: Structural insight into the function of human peptidyl arginine deiminase 6.
Authors: Williams, J.P.C. / Mouilleron, S. / Trapero, R.H. / Bertran, M.T. / Marsh, J.A. / Walport, L.J.
History
DepositionJun 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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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
B: Protein-arginine deiminase type-6


Theoretical massNumber of molelcules
Total (without water)155,6122
Polymers155,6122
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-23 kcal/mol
Surface area53570 Å2
Unit cell
Length a, b, c (Å)104.044, 123.332, 126.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#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: 77806.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI6, PAD6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6TGC4, protein-arginine deiminase

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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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20.9% w/v PEG3350, 0.2 M KSCN, 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: Feb 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.44→54.06 Å / Num. obs: 61221 / % possible obs: 99.19 % / Redundancy: 13.8 % / Biso Wilson estimate: 58.14 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.36 / Net I/σ(I): 4.98
Reflection shellResolution: 2.44→2.52 Å / Rmerge(I) obs: 5.62 / Num. unique obs: 6051 / CC1/2: 0.39

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
DIALSdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→54.06 Å / SU ML: 0.5279 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.7148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3074 3026 4.98 %
Rwork0.2581 57703 -
obs0.2606 60729 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.28 Å2
Refinement stepCycle: LAST / Resolution: 2.44→54.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10224 0 0 0 10224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003510457
X-RAY DIFFRACTIONf_angle_d0.609414223
X-RAY DIFFRACTIONf_chiral_restr0.04461629
X-RAY DIFFRACTIONf_plane_restr0.00521819
X-RAY DIFFRACTIONf_dihedral_angle_d4.84131411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.480.51321440.49112428X-RAY DIFFRACTION93.49
2.48-2.520.49531500.4692529X-RAY DIFFRACTION98.06
2.52-2.560.471260.45292615X-RAY DIFFRACTION98.6
2.56-2.610.48791350.43272556X-RAY DIFFRACTION99.04
2.61-2.660.44091320.41872590X-RAY DIFFRACTION99.2
2.66-2.710.41821160.40432596X-RAY DIFFRACTION99.16
2.71-2.770.45381370.39342607X-RAY DIFFRACTION99.24
2.77-2.840.39441460.37592581X-RAY DIFFRACTION99.53
2.84-2.910.36181420.33062609X-RAY DIFFRACTION99.42
2.91-2.990.4111240.34322634X-RAY DIFFRACTION99.32
2.99-3.070.36411160.33432613X-RAY DIFFRACTION99.42
3.07-3.170.37531610.3282604X-RAY DIFFRACTION99.64
3.17-3.290.43011240.3112643X-RAY DIFFRACTION99.75
3.29-3.420.31631120.29032667X-RAY DIFFRACTION99.82
3.42-3.570.30021330.26592629X-RAY DIFFRACTION99.75
3.57-3.760.32331530.26032607X-RAY DIFFRACTION99.64
3.76-40.27241290.22382666X-RAY DIFFRACTION99.68
4-4.310.24571400.21042649X-RAY DIFFRACTION99.93
4.31-4.740.23671340.1782691X-RAY DIFFRACTION100
4.74-5.420.23561490.18062670X-RAY DIFFRACTION100
5.43-6.830.29241520.2132707X-RAY DIFFRACTION99.93
6.83-54.060.25161710.20442812X-RAY DIFFRACTION99.63
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)
10.208540097741-0.145027591664-0.1403152497260.1149508172570.1259295230450.116272844709-0.02010992713110.117285737748-0.0452885435301-0.0693806222392-0.0808866591489-0.0801348422795-0.0319203876230.0869765366333-3.2452297127E-50.563090102236-0.04295273644430.04785550478350.547543564414-0.02271787086840.54306244402225.896232520423.3916330761-47.0387151025
20.4682358038560.351914477359-0.1840835097040.673715271614-0.001515177427470.2386920352160.0682816236737-0.02526967358280.1806727418790.01423047244870.001517903042560.0146371536318-0.2780909926140.0159100768143-0.000255047334840.4818255936860.05318427268040.02013710080910.405258964166-0.04418114995910.4907201282918.2414317602538.8341515227-14.6882510797
30.381662760960.2522653083120.09700822290470.3978849935230.2535039597510.331327982880.0421183033711-0.1044745717320.02642257297830.209601829731-0.0872652886634-0.01064077451-0.110197776878-0.257566079652-7.627778729E-60.654808537736-0.03000148370860.02976003141630.77361305834-0.004085503604010.527606319194-0.24293091143319.702179331615.060861854
40.136072146809-0.1378302891580.02576282594220.132068750516-0.04203500888310.0565551530971-0.1135476104970.08096127525360.001344887804640.07288140660450.09337580899460.02345410821450.390441788685-0.0376352734466-5.97318856814E-50.602952496791-0.0223955424409-0.02740823904610.6642646048990.02310780667210.6415615409114.00049836241-7.8536378280912.0899055323
50.2649212775280.03575772849070.1787932563310.291093525329-0.1243823078780.4458351623120.0109912721788-0.00216230369967-0.0110803352437-0.109974083586-0.04311451209280.0116963337203-0.00113793338234-0.1175552191220.001800820948250.416667481568-0.0451014904616-0.0283693921410.463850455154-0.003930009388790.50192684817-7.4230887361712.8312998205-39.1982205219
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 156 )AA7 - 1561 - 143
22chain 'A' and (resid 157 through 407 )AA157 - 407144 - 376
33chain 'A' and (resid 408 through 694 )AA408 - 694377 - 663
44chain 'B' and (resid 8 through 146 )BB8 - 1461 - 131
55chain 'B' and (resid 147 through 694 )BB147 - 694132 - 666

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