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- PDB-2dex: Crystal structure of human peptidylarginine deiminase 4 in comple... -

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Basic information

Entry
Database: PDB / ID: 2dex
TitleCrystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal peptide including Arg17
Components
  • 10-mer peptide from histone H3
  • Protein-arginine deiminase type IV
KeywordsHYDROLASE / histone modification enzyme
Function / homology
Function and homology information


histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification ...histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification / protein modification process / nucleosome assembly / chromatin organization / chromatin remodeling / innate immune response / calcium ion binding / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein-arginine deiminase, central domain / Protein-arginine deiminase, N-terminal domain / 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, central domain / Protein-arginine deiminase, N-terminal domain / 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 / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein-arginine deiminase type-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsArita, K. / Shimizu, T. / Hashimoto, H. / Hidaka, Y. / Yamada, M. / Sato, M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4
Authors: Arita, K. / Shimizu, T. / Hashimoto, H. / Hidaka, Y. / Yamada, M. / Sato, M.
History
DepositionFeb 18, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 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
X: Protein-arginine deiminase type IV
A: 10-mer peptide from histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,55110
Polymers76,0622
Non-polymers4898
Water3,459192
1
X: Protein-arginine deiminase type IV
A: 10-mer peptide from histone H3
hetero molecules

X: Protein-arginine deiminase type IV
A: 10-mer peptide from histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,10220
Polymers152,1244
Non-polymers97716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7760 Å2
ΔGint-200 kcal/mol
Surface area50650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)146.072, 60.103, 115.703
Angle α, β, γ (deg.)90.00, 124.32, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis: -x, y, -z.

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Components

#1: Protein Protein-arginine deiminase type IV / Peptidylarginine deiminase IV / HL-60 PAD / peptidylarginine deiminase 4


Mass: 74933.836 Da / Num. of mol.: 1 / Mutation: C645A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI4, PADI5, PDI5 / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UM07, protein-arginine deiminase
#2: Protein/peptide 10-mer peptide from histone H3


Mass: 1128.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Imidazole (pH8.0), 0.2M lithium sulfate, 10% PEGMME2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 1, 2004
RadiationMonochromator: undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→33.13 Å / Num. obs: 46064 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.17 Å / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WDA

1wda


Resolution: 2.1→33.13 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 13.03 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.225 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24698 4628 10 %RANDOM
Rwork0.20251 ---
all0.27 45630 --
obs0.20698 41436 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.994 Å2
Baniso -1Baniso -2Baniso -3
1--5.45 Å20 Å2-3.85 Å2
2--4.69 Å20 Å2
3----3.58 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4978 0 20 192 5190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225109
X-RAY DIFFRACTIONr_bond_other_d0.0010.024613
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9726934
X-RAY DIFFRACTIONr_angle_other_deg0.969310796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8335626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36324.529223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58715876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8961526
X-RAY DIFFRACTIONr_chiral_restr0.0980.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025588
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02980
X-RAY DIFFRACTIONr_nbd_refined0.210.2975
X-RAY DIFFRACTIONr_nbd_other0.1840.24833
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22411
X-RAY DIFFRACTIONr_nbtor_other0.0890.23079
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2232
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0830.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.218
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2040.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.691.53267
X-RAY DIFFRACTIONr_mcbond_other0.1241.51263
X-RAY DIFFRACTIONr_mcangle_it1.14125140
X-RAY DIFFRACTIONr_scbond_it1.4932112
X-RAY DIFFRACTIONr_scangle_it2.2894.51794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 262 -
Rwork0.255 2413 -
obs--74.51 %
Refinement TLS params.Method: refined / Origin x: 16.4591 Å / Origin y: 34.1315 Å / Origin z: 0.9303 Å
111213212223313233
T-0.1248 Å2-0.0021 Å20.0153 Å2--0.0655 Å20.0435 Å2---0.0665 Å2
L1.094 °20.0919 °21.1961 °2-0.223 °20.3156 °2--3.0352 °2
S-0.0144 Å °0.1255 Å °0.0612 Å °0.0304 Å °-0.0273 Å °-0.07 Å °0.0726 Å °0.372 Å °0.0416 Å °

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