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- PDB-1wd8: Calcium free form of human peptidylarginine deiminase type4 (PAD4) -

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Basic information

Entry
Database: PDB / ID: 1wd8
TitleCalcium free 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 / SYNCHROTRON / MIR / Resolution: 2.8 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 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-arginine deiminase type IV


Theoretical massNumber of molelcules
Total (without water)74,8181
Polymers74,8181
Non-polymers00
Water0
1
A: Protein-arginine deiminase type IV

A: Protein-arginine deiminase type IV


Theoretical massNumber of molelcules
Total (without water)149,6352
Polymers149,6352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)144.612, 60.437, 113.488
Angle α, β, γ (deg.)90.00, 123.61, 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: 74817.742 Da / Num. of mol.: 1
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

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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: 2.56 Å3/Da / Density % sol: 56.1 %
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: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 18, 2002
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→95.35 Å / Num. obs: 20164 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 89.3 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.68 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3980 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→33.44 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.902 / SU B: 14.486 / SU ML: 0.282 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.252 / ESU R Free: 0.384 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26444 1961 10 %RANDOM
Rwork0.23084 ---
all0.23428 17603 --
obs0.23428 17603 95.93 %-
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: 64.342 Å2
Baniso -1Baniso -2Baniso -3
1--5.16 Å20 Å2-3.54 Å2
2--5.89 Å20 Å2
3----4.64 Å2
Refinement stepCycle: LAST / Resolution: 2.8→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 0 0 4382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214398
X-RAY DIFFRACTIONr_bond_other_d0.0020.023980
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9585980
X-RAY DIFFRACTIONr_angle_other_deg0.97139268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0265547
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_restr0.0990.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024822
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02846
X-RAY DIFFRACTIONr_nbd_refined0.2340.2938
X-RAY DIFFRACTIONr_nbd_other0.2410.24853
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0970.22728
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9151.52788
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71224507
X-RAY DIFFRACTIONr_scbond_it1.88731610
X-RAY DIFFRACTIONr_scangle_it3.2354.51473
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.367 146
Rwork0.318 1288
Refinement TLS params.Method: refined / Origin x: 14.8809 Å / Origin y: 29.1129 Å / Origin z: -0.8153 Å
111213212223313233
T0.0666 Å20.0157 Å20.0052 Å2-0.0233 Å20.0311 Å2--0.0459 Å2
L0.6305 °20.0343 °20.8225 °2-0.0647 °20.1896 °2--2.2448 °2
S-0.0162 Å °0.1086 Å °0.0876 Å °-0.0023 Å °-0.0988 Å °-0.0231 Å °0.0908 Å °0.2876 Å °0.115 Å °

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