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- PDB-4x8g: Crystal structure of human peptidylarginine deiminase type4 (PAD4... -

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Basic information

Entry
Database: PDB / ID: 4x8g
TitleCrystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with GSK199
ComponentsProtein-arginine deiminase type-4
KeywordsHydrolase/Hydrolase Inhibitor / 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
Chem-3Z0 / Protein-arginine deiminase type-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.29 Å
AuthorsLewis, H.D. / Bax, B.D. / Chung, C.-W. / Polyakova, O. / Thorpe, J.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Inhibition of PAD4 activity is sufficient to disrupt mouse and human NET formation.
Authors: Lewis, H.D. / Liddle, J. / Coote, J.E. / Atkinson, S.J. / Barker, M.D. / Bax, B.D. / Bicker, K.L. / Bingham, R.P. / Campbell, M. / Chen, Y.H. / Chung, C.W. / Craggs, P.D. / Davis, R.P. / ...Authors: Lewis, H.D. / Liddle, J. / Coote, J.E. / Atkinson, S.J. / Barker, M.D. / Bax, B.D. / Bicker, K.L. / Bingham, R.P. / Campbell, M. / Chen, Y.H. / Chung, C.W. / Craggs, P.D. / Davis, R.P. / Eberhard, D. / Joberty, G. / Lind, K.E. / Locke, K. / Maller, C. / Martinod, K. / Patten, C. / Polyakova, O. / Rise, C.E. / Rudiger, M. / Sheppard, R.J. / Slade, D.J. / Thomas, P. / Thorpe, J. / Yao, G. / Drewes, G. / Wagner, D.D. / Thompson, P.R. / Prinjha, R.K. / Wilson, D.M.
History
DepositionDec 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)75,5116
Polymers74,9181
Non-polymers5935
Water43224
1
A: Protein-arginine deiminase type-4
hetero molecules

A: Protein-arginine deiminase type-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,02112
Polymers149,8362
Non-polymers1,18610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5000 Å2
ΔGint-84 kcal/mol
Surface area50210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.990, 62.250, 116.750
Angle α, β, γ (deg.)90.00, 124.71, 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: 74917.836 Da / Num. of mol.: 1 / Mutation: C645A
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-Gold(DE3)pLysS AG / References: UniProt: Q9UM07, protein-arginine deiminase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-3Z0 / [(3R)-3-aminopiperidin-1-yl][2-(1-ethyl-1H-pyrrolo[2,3-b]pyridin-2-yl)-7-methoxy-1-methyl-1H-benzimidazol-5-yl]methanone


Mass: 432.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28N6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.8
Details: 100 mM imidazole, pH 7.8, 200 mM Li2SO4, 2 mM TCEP, 6-7.5% PEG 2K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.29→19.86 Å / Num. obs: 13385 / % possible obs: 97.6 % / Redundancy: 3.3 % / Net I/σ(I): 9.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
REFMACrefinement
BUSTERrefinement
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.29→19.86 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 648 4.84 %
Rwork0.1984 --
obs0.2 13383 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.29→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4502 0 36 24 4562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024641
X-RAY DIFFRACTIONf_angle_d0.566344
X-RAY DIFFRACTIONf_dihedral_angle_d13.171595
X-RAY DIFFRACTIONf_chiral_restr0.023738
X-RAY DIFFRACTIONf_plane_restr0.004825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.54320.29671160.29682587X-RAY DIFFRACTION99
3.5432-3.89740.29331460.25032525X-RAY DIFFRACTION98
3.8974-4.45580.22371190.20722524X-RAY DIFFRACTION98
4.4558-5.5930.24921120.17992524X-RAY DIFFRACTION96
5.593-19.86380.19861550.1752575X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.47331.65822.9451.04690.81753.612-0.4031.4954-0.2705-0.574-0.1084-0.01830.0959-0.68980.17481.7343-0.02670.03162.0214-0.35780.8633-9.7117.3624-41.7024
23.9161-0.67740.55571.23110.589.0332-0.00651.10860.4808-0.4860.036-0.3001-0.44271.3601-0.0231.1522-0.1570.1160.90760.24820.884411.294836.1562-21.4602
33.7262-4.0184-0.53185.2056-0.48911.3807-0.3637-0.8090.72190.75240.0195-1.4082-0.40922.59630.97581.2638-0.2526-0.07552.7192-0.03461.586341.016239.985112.7575
42.6225-1.0769-2.04634.56884.70977.2074-0.11980.2171.5522-0.83840.69970.1186-1.79621.7137-0.56221.3164-0.3720.02151.2528-0.04561.302623.558840.5382-0.303
55.6411-0.28451.32371.42711.17139.31590.0218-0.84690.51180.07790.05950.0604-0.06960.9182-0.05631.0844-0.10240.01660.7926-0.04890.862114.724633.804816.2826
63.50421.6442.47632.1279-0.13495.19020.307-1.74890.15230.6978-0.1237-0.67160.68971.7922-0.06381.198-0.0105-0.23452.1964-0.27921.039527.283633.296432.9717
70.2749-0.7428-0.05121.98620.14160.0088-0.6761.47611.3517-2.9550.50810.0726-0.45720.5027-0.25091.1628-0.5661-0.09272.1024-0.30861.43429.434650.413322.9636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:112 )A3 - 112
2X-RAY DIFFRACTION2( CHAIN A AND RESID 113:292 )A113 - 292
3X-RAY DIFFRACTION3( CHAIN A AND RESID 308:336 )A308 - 336
4X-RAY DIFFRACTION4( CHAIN A AND RESID 351:393 )A351 - 393
5X-RAY DIFFRACTION5( CHAIN A AND RESID 405:492 )A405 - 492
6X-RAY DIFFRACTION6( CHAIN A AND RESID 495:630 )A495 - 630
7X-RAY DIFFRACTION7( CHAIN A AND RESID 634:645 )A634 - 645

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