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

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Basic information

Entry
Database: PDB / ID: 2dey
TitleCrystal structure of human peptidylarginine deiminase 4 in complex with histone H4 N-terminal tail including Arg3
Components
  • 10-mer peptide from histone H4
  • 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: 2.25 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 / 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.pdbx_leaving_atom_flag / _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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,36810
Polymers75,8792
Non-polymers4898
Water2,774154
1
X: Protein-arginine deiminase type IV
A: 10-mer peptide from histone H4
hetero molecules

X: Protein-arginine deiminase type IV
A: 10-mer peptide from histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,73520
Polymers151,7584
Non-polymers97716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)146.192, 60.611, 115.203
Angle α, β, γ (deg.)90.00, 124.18, 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 H4


Mass: 945.101 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.: 154 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 56.6 %
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: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2004
RadiationMonochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→33.57 Å / Num. obs: 39243 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.25→2.33 Å / % possible all: 98.3

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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: 2.25→33.57 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 18.427 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.277 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24846 3918 10 %RANDOM
Rwork0.19946 ---
all0.275 39238 --
obs0.20443 35325 98.3 %-
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: 55.294 Å2
Baniso -1Baniso -2Baniso -3
1--4.67 Å20 Å2-3.39 Å2
2--4.3 Å20 Å2
3----3.44 Å2
Refinement stepCycle: LAST / Resolution: 2.25→33.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 20 154 5154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225111
X-RAY DIFFRACTIONr_bond_other_d0.0020.024610
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9736935
X-RAY DIFFRACTIONr_angle_other_deg0.872310787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3975627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35624.505222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.01515876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8371526
X-RAY DIFFRACTIONr_chiral_restr0.0950.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025594
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02982
X-RAY DIFFRACTIONr_nbd_refined0.210.21000
X-RAY DIFFRACTIONr_nbd_other0.1890.24815
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22388
X-RAY DIFFRACTIONr_nbtor_other0.090.23066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0650.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.216
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1450.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4480.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7481.53268
X-RAY DIFFRACTIONr_mcbond_other0.1341.51266
X-RAY DIFFRACTIONr_mcangle_it1.22825146
X-RAY DIFFRACTIONr_scbond_it1.59932111
X-RAY DIFFRACTIONr_scangle_it2.4444.51789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 274 -
Rwork0.297 2574 -
obs--97.87 %
Refinement TLS params.Method: refined / Origin x: 16.4467 Å / Origin y: 34.5896 Å / Origin z: 0.8419 Å
111213212223313233
T-0.1344 Å20.0119 Å20.0242 Å2--0.1337 Å20.0539 Å2---0.0819 Å2
L1.2857 °20.0926 °21.4489 °2-0.1635 °20.3986 °2--3.9697 °2
S-0.0236 Å °0.2165 Å °0.1044 Å °0.0145 Å °-0.0507 Å °-0.0775 Å °0.1108 Å °0.5998 Å °0.0743 Å °

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