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- PDB-1wd9: Calcium bound form of human peptidylarginine deiminase type4 (PAD4) -

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Basic information

Entry
Database: PDB / ID: 1wd9
TitleCalcium bound form of human peptidylarginine deiminase type4 (PAD4)
ComponentsProtein-arginine deiminase type IV
KeywordsHYDROLASE / Post-translational 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 / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsArita, K. / Hashimoto, H. / Shimizu, T. / Nakashima, K. / Yamada, M. / Sato, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural basis for Ca(2+)-induced activation of human PAD4
Authors: Arita, K. / Hashimoto, H. / Shimizu, T. / Nakashima, K. / Yamada, M. / Sato, M.
History
DepositionMay 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2004Provider: 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_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_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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,2749
Polymers74,7861
Non-polymers4898
Water1,15364
1
A: Protein-arginine deiminase type IV
hetero molecules

A: Protein-arginine deiminase type IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,54918
Polymers149,5712
Non-polymers97716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)146.389, 60.094, 115.339
Angle α, β, γ (deg.)90.00, 124.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 74785.680 Da / Num. of mol.: 1 / Mutation: C645A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UM07, protein-arginine deiminase
#2: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.83 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEGMME2000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 2, 2004
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→22.8 Å / Num. all: 24864 / Num. obs: 24864 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 72.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.1
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 8.7 / Num. unique all: 2485 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→22.8 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.902 / SU B: 11.326 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.779 / ESU R Free: 0.342 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26885 2495 10.1 %RANDOM
Rwork0.2237 ---
all0.22828 22280 --
obs0.22828 22280 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.69 Å2
Baniso -1Baniso -2Baniso -3
1--6.14 Å20 Å2-4.22 Å2
2--6.13 Å20 Å2
3----4.75 Å2
Refinement stepCycle: LAST / Resolution: 2.6→22.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4745 0 20 64 4829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224869
X-RAY DIFFRACTIONr_bond_other_d0.0020.024393
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9616609
X-RAY DIFFRACTIONr_angle_other_deg1.05310272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.285594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025309
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02942
X-RAY DIFFRACTIONr_nbd_refined0.2140.2975
X-RAY DIFFRACTIONr_nbd_other0.2360.25240
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0940.22977
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0930.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0580.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7371.53012
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3724894
X-RAY DIFFRACTIONr_scbond_it1.74831857
X-RAY DIFFRACTIONr_scangle_it2.9144.51715
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.338 206
Rwork0.298 1625
Refinement TLS params.Method: refined / Origin x: 16.0365 Å / Origin y: 31.4518 Å / Origin z: 0.3174 Å
111213212223313233
T0.076 Å2-0.0032 Å20.0237 Å2-0.0251 Å20.0465 Å2--0.0977 Å2
L0.867 °20.0159 °21.063 °2-0.0779 °20.2939 °2--2.6703 °2
S-0.0206 Å °0.1241 Å °0.0795 Å °-0.0123 Å °-0.0573 Å °-0.0508 Å °0.0982 Å °0.3323 Å °0.0779 Å °

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