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- PDB-4n2f: Crystal structure of Protein Arginine Deiminase 2 (D169A, 0 mM Ca2+) -

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Basic information

Entry
Database: PDB / ID: 4n2f
TitleCrystal structure of Protein Arginine Deiminase 2 (D169A, 0 mM Ca2+)
ComponentsProtein-arginine deiminase type-2
KeywordsHYDROLASE / deiminase
Function / homology
Function and homology information


negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / negative regulation of chemokine-mediated signaling pathway / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / Chromatin modifying enzymes / estrogen receptor signaling pathway / substantia nigra development / transcription initiation-coupled chromatin remodeling ...negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / negative regulation of chemokine-mediated signaling pathway / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / Chromatin modifying enzymes / estrogen receptor signaling pathway / substantia nigra development / transcription initiation-coupled chromatin remodeling / cellular response to leukemia inhibitory factor / nuclear estrogen receptor binding / euchromatin / azurophil granule lumen / chromatin remodeling / calcium ion binding / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / extracellular region / 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
ACETATE ION / Protein-arginine deiminase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSlade, D.J. / Zhang, X. / Fang, P. / Dreyton, C.J. / Zhang, Y. / Gross, M.L. / Guo, M. / Coonrod, S.A. / Thompson, P.R.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Protein arginine deiminase 2 binds calcium in an ordered fashion: implications for inhibitor design.
Authors: Slade, D.J. / Fang, P. / Dreyton, C.J. / Zhang, Y. / Fuhrmann, J. / Rempel, D. / Bax, B.D. / Coonrod, S.A. / Lewis, H.D. / Guo, M. / Gross, M.L. / Thompson, P.R.
History
DepositionOct 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Sep 20, 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.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.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_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

Downloads & links

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Assembly

Deposited unit
A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2418
Polymers78,6291
Non-polymers6127
Water8,773487
1
A: Protein-arginine deiminase type-2
hetero molecules

A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,48216
Polymers157,2582
Non-polymers1,22414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area8400 Å2
ΔGint-165 kcal/mol
Surface area51850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.780, 51.020, 75.840
Angle α, β, γ (deg.)90.000, 105.640, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein-arginine deiminase type-2 / PAD-H19 / Peptidylarginine deiminase II / Protein-arginine deiminase type II


Mass: 78629.000 Da / Num. of mol.: 1 / Mutation: D169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI2, KIAA0994, PDI2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2J8, protein-arginine deiminase
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.6
Details: 10-20% MPD, 50 mM MES, pH 5.6, 0.12 M sodium acetate, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2010 / Details: beryllium lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.8→37.699 Å / Num. obs: 69618 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 21.92 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.9
Reflection shellHighest resolution: 1.8 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4N20

4n20


Resolution: 1.8→37.699 Å / Occupancy max: 1 / Occupancy min: 0.14 / FOM work R set: 0.8737 / SU ML: 0.42 / σ(F): 1.34 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 3514 5.05 %
Rwork0.171 --
obs0.1726 69618 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.932 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 107.6 Å2 / Biso mean: 30.7463 Å2 / Biso min: 10.08 Å2
Baniso -1Baniso -2Baniso -3
1--4.9612 Å20 Å2-2.5555 Å2
2--5.4605 Å20 Å2
3----0.4993 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4954 0 38 487 5479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095228
X-RAY DIFFRACTIONf_angle_d1.2157135
X-RAY DIFFRACTIONf_chiral_restr0.104792
X-RAY DIFFRACTIONf_plane_restr0.007913
X-RAY DIFFRACTIONf_dihedral_angle_d13.1691903
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.86430.27333610.228565706931
1.8643-1.9390.27313630.200965296892
1.939-2.02720.21283580.175365426900
2.0272-2.13410.21143430.160566066949
2.1341-2.26780.19943230.16865946917
2.2678-2.44290.23213540.171666056959
2.4429-2.68860.22543450.180765956940
2.6886-3.07750.20243440.174266096953
3.0775-3.87670.17223650.157266557020
3.8767-37.70740.18143580.166667997157
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)
13.4921-1.48741.37852.0402-0.20654.07610.15410.0650.0767-0.2842-0.08070.1178-0.24940.0303-0.0830.20260.02240.00410.1023-0.04950.1769139.252413.599769.6547
25.861-1.54372.59542.3749-0.70821.78610.59120.0929-0.1684-0.6337-0.19250.65680.3291-0.3486-0.3220.3190.0886-0.14370.1715-0.07660.3351127.009712.020663.8343
36.3281-0.43541.92030.2276-0.35010.7227-0.0578-0.32460.49980.0114-0.095-0.1486-0.0312-0.00340.14610.17860.0223-0.01030.2593-0.0010.2262167.64037.389387.1817
47.4159-1.17923.88414.0052-0.60054.0207-0.0235-1.19550.11790.2931-0.0176-0.17970.0576-0.0723-0.00390.22430.03540.01390.42680.04120.071157.2752.017693.4176
51.16280.15690.31591.22950.2011.10820.0355-1.0363-0.74650.31060.05920.0790.1768-0.0689-0.02890.2175-0.0345-0.01320.42780.12320.2562158.2518-8.278289.118
63.1344-0.40391.60020.17170.09951.16580.0552-0.1418-0.33710.00950.04330.05470.1062-0.0858-0.10230.131-0.0080.01560.16150.04640.1569173.8428-3.441889.3952
75.5867-0.22450.49464.15741.0155.3627-0.1993-0.5161-0.29080.24410.06610.49080.2259-0.62560.11040.31130.04490.05180.29890.02320.1696201.3307-7.438110.5369
87.129-6.0982.45118.3091-2.57562.5097-0.056-0.7417-0.0923-0.03050.21710.0670.0285-0.4246-0.13590.13690.00540.01530.25370.01680.1724189.3246-4.459397.9565
95.1201-5.07044.88875.0156-4.83234.6627-0.5555-0.6336-1.83810.57130.65021.21631.8980.5032-0.13110.57090.12920.06810.3650.04640.6928194.1178-18.717995.7614
108.7318-2.1934-2.95755.87470.24262.877-0.5238-0.7629-1.12221.60280.5610.21311.0357-0.0582-0.05650.49830.0154-0.02380.50910.13980.4055187.5954-12.169898.7681
113.5503-1.1444-0.28561.47730.17671.19340.03390.2367-0.0788-0.146-0.04670.07760.0402-0.11020.00940.1468-0.010.00870.13840.02150.1106199.8375-3.784484.3699
123.4593-0.85011.02831.1571-0.49521.7413-0.18520.08490.26370.10050.0128-0.0163-0.30270.07580.0940.157-0.0088-0.00620.0544-0.00310.1077220.24173.959295.8295
135.63444.3274-4.39286.1933-4.83584.8654-0.094-0.4169-0.51590.0439-0.0955-0.46410.26970.51140.14140.14710.0276-0.01150.13520.01220.1414228.3458-12.9388103.3016
142.0327-0.08480.24740.7064-0.17751.517-0.0610.17450.0085-0.02610.0276-0.0208-0.00020.10050.03410.1338-0.01940.01240.0841-0.01050.1045216.2553-2.103491.029
152.2887-1.02050.04654.2435-0.40741.6912-0.095-0.2336-0.03130.10.09880.1225-0.072-0.002-0.0060.15420.01380.00340.1366-0.01010.0803217.8142-1.2504105.3566
163.8519-2.32372.03792.7841-1.56751.9031-0.01580.18410.0467-0.0323-0.0235-0.0170.12260.01810.07110.15030.02890.03230.2127-0.00920.2218191.01193.891193.9279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:96)A2 - 96
2X-RAY DIFFRACTION2(chain A and resid 97:112)A97 - 112
3X-RAY DIFFRACTION3(chain A and resid 113:156)A113 - 156
4X-RAY DIFFRACTION4(chain A and resid 178:193)A178 - 193
5X-RAY DIFFRACTION5(chain A and resid 194:242)A194 - 242
6X-RAY DIFFRACTION6(chain A and resid 243:318)A243 - 318
7X-RAY DIFFRACTION7(chain A and resid 319:346)A319 - 346
8X-RAY DIFFRACTION8(chain A and resid 347:369)A347 - 369
9X-RAY DIFFRACTION9(chain A and resid 370:375)A370 - 375
10X-RAY DIFFRACTION10(chain A and resid 384:402)A384 - 402
11X-RAY DIFFRACTION11(chain A and resid 403:475)A403 - 475
12X-RAY DIFFRACTION12(chain A and resid 476:514)A476 - 514
13X-RAY DIFFRACTION13(chain A and resid 515:530)A515 - 530
14X-RAY DIFFRACTION14(chain A and resid 531:607)A531 - 607
15X-RAY DIFFRACTION15(chain A and resid 608:644)A608 - 644
16X-RAY DIFFRACTION16(chain A and resid 645:667)A645 - 667

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