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- PDB-3b1t: Crystal structure of human peptidylarginine deiminase 4 in comple... -

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Basic information

Entry
Database: PDB / ID: 3b1t
TitleCrystal structure of human peptidylarginine deiminase 4 in complex with o-Cl-amidine
ComponentsProtein-arginine deiminase type-4
KeywordsHYDROLASE/HYDROLASE INHIBITOR / nuclei / 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 / 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-YCL / Protein-arginine deiminase type-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCausey, C.P. / Jones, J.E. / Slack, J.L. / Kamei, D. / Jones Jr, L.E. / Subramanian, V. / Knuckley, B. / Ebrahimi, P. / Chumanevich, A.A. / Luo, Y. ...Causey, C.P. / Jones, J.E. / Slack, J.L. / Kamei, D. / Jones Jr, L.E. / Subramanian, V. / Knuckley, B. / Ebrahimi, P. / Chumanevich, A.A. / Luo, Y. / Hashimoto, H. / Shimizu, T. / Sato, M. / Hofseth, L.J. / Thompson, P.R.
CitationJournal: J.Med.Chem. / Year: 2011
Title: The Development of N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-fluoro-1-iminoethyl)-l-ornithine Amide (o-F-amidine) and N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-chloro-1-iminoethyl)-l-ornithine Amide (o-Cl- ...Title: The Development of N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-fluoro-1-iminoethyl)-l-ornithine Amide (o-F-amidine) and N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-chloro-1-iminoethyl)-l-ornithine Amide (o-Cl-amidine) As Second Generation Protein Arginine Deiminase (PAD) Inhibitors
Authors: Causey, C.P. / Jones, J.E. / Slack, J.L. / Kamei, D. / Jones Jr, L.E. / Subramanian, V. / Knuckley, B. / Ebrahimi, P. / Chumanevich, A.A. / Luo, Y. / Hashimoto, H. / Sato, M. / Hofseth, L.J. / Thompson, P.R.
History
DepositionJul 13, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_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.conn_type_id / _struct_conn.id / _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_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

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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)75,80910
Polymers74,9661
Non-polymers8439
Water2,774154
1
A: Protein-arginine deiminase type-4
hetero molecules

A: Protein-arginine deiminase type-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,61920
Polymers149,9322
Non-polymers1,68718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6190 Å2
ΔGint-181 kcal/mol
Surface area50420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.787, 60.853, 114.302
Angle α, β, γ (deg.)90.00, 123.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UM07, protein-arginine deiminase
#2: Chemical ChemComp-YCL / 2-{[(2S)-1-amino-5-{[(1Z)-2-chloroethanimidoyl]amino}-1-oxopentan-2-yl]carbamoyl}benzoic acid / o-Cl-amidine


Mass: 354.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19ClN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsG55S, V82A AND G112A ARE NATURAL VARIANTS BASED ON REF 1 AND 4 OF DATABASE UNIPROT/SWISS-PROT ...G55S, V82A AND G112A ARE NATURAL VARIANTS BASED ON REF 1 AND 4 OF DATABASE UNIPROT/SWISS-PROT Q9UM07 (PADI4_HUMAN).

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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: 56.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 27393

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Processing

SoftwareName: REFMAC / Version: 5.6.0085 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WDA

1wda


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 21.016 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.516 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2629 1367 5 %RANDOM
Rwork0.2111 ---
obs0.2138 27346 100 %-
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: 75.845 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å20 Å2-1.86 Å2
2--2.18 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4912 0 43 154 5109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225065
X-RAY DIFFRACTIONr_bond_other_d00.023453
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9766876
X-RAY DIFFRACTIONr_angle_other_deg3.37938450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4555618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69724.57221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.07915858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2191525
X-RAY DIFFRACTIONr_chiral_restr0.0860.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215548
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02975
LS refinement shellResolution: 2.504→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 63 -
Rwork0.303 1480 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -16.4735 Å / Origin y: -0.1334 Å / Origin z: -1.1262 Å
111213212223313233
T0.0187 Å20.0031 Å2-0.018 Å2-0.2719 Å2-0.0731 Å2--0.0994 Å2
L1.3963 °2-0.0805 °21.6896 °2-0.2724 °2-0.382 °2--4.7812 °2
S-0.069 Å °-0.2305 Å °0.1263 Å °0.0008 Å °-0.0712 Å °0.1091 Å °0.0421 Å °-0.6034 Å °0.1402 Å °

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