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- PDB-2dw5: Crystal structure of human peptidylarginine deiminase 4 in comple... -

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Basic information

Entry
Database: PDB / ID: 2dw5
TitleCrystal structure of human peptidylarginine deiminase 4 in complex with N-alpha-benzoyl-N5-(2-fluoro-1-iminoethyl)-L-ornithine amide
ComponentsProtein-arginine deiminase type-4
KeywordsHYDROLASE / protein-inhibitor complex
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
Chem-BFB / Protein-arginine deiminase type-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLuo, Y. / Arita, K. / Sato, M. / Thompson, P.R.
CitationJournal: Biochemistry / Year: 2006
Title: Inhibitors and Inactivators of Protein Arginine Deiminase 4: Functional and Structural Characterization
Authors: Luo, Y. / Arita, K. / Bhatia, M. / Knuckley, B. / Lee, Y.H. / Stallcup, M.R. / Sato, M. / Thompson, P.R.
History
DepositionAug 4, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-arginine deiminase type-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,73110
Polymers74,9661
Non-polymers7659
Water2,702150
1
A: Protein-arginine deiminase type-4
hetero molecules

A: Protein-arginine deiminase type-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,46220
Polymers149,9322
Non-polymers1,53018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)146.259, 60.516, 114.911
Angle α, β, γ (deg.)90.00, 124.19, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by -x, y, -z.

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Components

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


Mass: 74965.898 Da / Num. of mol.: 1
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: 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: Chemical ChemComp-BFB / N-[(1S)-1-(AMINOCARBONYL)-4-(ETHANIMIDOYLAMINO)BUTYL]BENZAMIDE / (S)-N-ALPHA-BENZOYL-N5-(2-FLUORO-1-IMINOETHYL)-L-ORNITHINE AMIDE


Mass: 276.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 56.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEGMME2000, 0.1M Imidazole PH 8.0, 0.2M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2005
RadiationMonochromator: UNDULATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→42.7 Å / Num. obs: 32324 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.38 Å / % possible all: 47.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WDA

1wda


Resolution: 2.3→42.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 16.413 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.311 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25204 1700 5 %RANDOM
Rwork0.19769 ---
all0.20048 ---
obs0.20048 31719 91.32 %-
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: 50.487 Å2
Baniso -1Baniso -2Baniso -3
1--6.05 Å20 Å2-4.12 Å2
2--5.7 Å20 Å2
3----4.27 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 40 150 5118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225064
X-RAY DIFFRACTIONr_bond_other_d0.0010.023436
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.9756862
X-RAY DIFFRACTIONr_angle_other_deg1.03338399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3685620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97624.682220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.61115844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5281524
X-RAY DIFFRACTIONr_chiral_restr0.1050.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02969
X-RAY DIFFRACTIONr_nbd_refined0.2140.2986
X-RAY DIFFRACTIONr_nbd_other0.2050.23545
X-RAY DIFFRACTIONr_nbtor_refined0.180.22370
X-RAY DIFFRACTIONr_nbtor_other0.0950.22745
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2195
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1270.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8111.53251
X-RAY DIFFRACTIONr_mcbond_other0.1431.51247
X-RAY DIFFRACTIONr_mcangle_it1.35825084
X-RAY DIFFRACTIONr_scbond_it1.88932097
X-RAY DIFFRACTIONr_scangle_it2.7454.51778
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 84 -
Rwork0.255 1676 -
obs--64 %
Refinement TLS params.Method: refined / Origin x: 16.447 Å / Origin y: 33.8756 Å / Origin z: 1.1603 Å
111213212223313233
T-0.0873 Å2-0.0081 Å20.0461 Å2--0.1598 Å20.0657 Å2---0.0315 Å2
L1.1922 °20.0565 °21.4711 °2-0.1638 °20.3717 °2--3.7347 °2
S-0.0355 Å °0.1717 Å °0.1223 Å °-0.0134 Å °-0.0662 Å °-0.0897 Å °0.1072 Å °0.5164 Å °0.1016 Å °

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