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

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Basic information

Entry
Database: PDB / ID: 4dkt
TitleCrystal structure of human peptidylarginine deiminase 4 in complex with N-acetyl-L-threonyl-L-alpha-aspartyl-N5-[(1E)-2-fluoroethanimidoyl]-L-ornithinamide
Components
  • Protein-arginine deiminase type-4
  • Thr-Asp-F-amidine
KeywordsHYDROLASE/HYDROLASE INHIBITOR / alpha/beta-propeller / immunoglobulin-like / arginine citrullination / post-translational / HYDROLASE-HYDROLASE 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 / 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
Thr-Asp-F-amidine / Protein-arginine deiminase type-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsJones, J.E. / Slack, J.L. / Fang, P. / Zhang, X. / Subramanian, V. / Causey, C.P. / Coonrod, S.A. / Guo, M. / Thompson, P.R.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Synthesis and Screening of a Haloacetamidine Containing Library To Identify PAD4 Selective Inhibitors.
Authors: Jones, J.E. / Slack, J.L. / Fang, P. / Zhang, X. / Subramanian, V. / Causey, C.P. / Coonrod, S.A. / Guo, M. / Thompson, P.R.
History
DepositionFeb 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-arginine deiminase type-4
B: Thr-Asp-F-amidine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,54111
Polymers75,0242
Non-polymers5179
Water66737
1
A: Protein-arginine deiminase type-4
B: Thr-Asp-F-amidine
hetero molecules

A: Protein-arginine deiminase type-4
B: Thr-Asp-F-amidine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,08122
Polymers150,0484
Non-polymers1,03318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)147.654, 61.079, 115.382
Angle α, β, γ (deg.)90.00, 124.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 74592.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI4, PADI5, PDI5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UM07, protein-arginine deiminase
#2: Protein/peptide Thr-Asp-F-amidine / N-acetyl-L-threonyl-L-alpha-aspartyl-N5-[(1E)-2-fluoroethanimidoyl]-L-ornithinamide / TDFA


Type: Peptide-like / Class: Inhibitor / Mass: 431.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: Thr-Asp-F-amidine

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Non-polymers , 4 types, 46 molecules

#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.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHR-ASP-F-AMIDINE IS AN N-TERMINALLY ACETYLATED, C-TERMINALLY AMIDATED TRIPEPTIDE.

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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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M imidazole, pH 8.0, 0.2 M lithium sulfate, 10% w/v PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2011
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.98→50 Å / Num. obs: 17606 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.08 / Χ2: 0.923 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.98-3.097.50.55517500.8631100
3.09-3.217.60.42817440.8741100
3.21-3.367.60.29217280.8841100
3.36-3.537.60.19417420.9241100
3.53-3.757.70.13517591.0021100
3.75-4.047.60.10117591.1181100
4.04-4.457.60.06817490.9311100
4.45-5.097.60.05517770.9741100
5.09-6.427.50.05417661.0411100
6.42-507.20.0318320.602199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WDA

1wda


Resolution: 2.98→41.442 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8419 / SU ML: 0.84 / σ(F): 1.36 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 860 5.1 %
Rwork0.1905 --
obs0.1925 16858 95.86 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.885 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso max: 123.72 Å2 / Biso mean: 44.4233 Å2 / Biso min: 8.86 Å2
Baniso -1Baniso -2Baniso -3
1--1.233 Å20 Å2-0.834 Å2
2--5.4847 Å20 Å2
3----4.2517 Å2
Refinement stepCycle: LAST / Resolution: 2.98→41.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5016 0 23 37 5076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065150
X-RAY DIFFRACTIONf_angle_d1.0496988
X-RAY DIFFRACTIONf_chiral_restr0.073779
X-RAY DIFFRACTIONf_plane_restr0.005904
X-RAY DIFFRACTIONf_dihedral_angle_d15.6651914
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.98-3.16670.29591180.25052127224577
3.1667-3.41110.25121460.22162697284398
3.4111-3.75420.26411540.192727482902100
3.7542-4.29690.20821480.16927742922100
4.2969-5.41180.20151580.157627852943100
5.4118-41.44560.21621360.203628673003100

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