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- PDB-4n2b: Crystal structure of Protein Arginine Deiminase 2 (10 mM Ca2+) -

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Basic information

Entry
Database: PDB / ID: 4n2b
TitleCrystal structure of Protein Arginine Deiminase 2 (10 mM Ca2+)
ComponentsProtein-arginine deiminase type-2
KeywordsHYDROLASE / deiminase
Function / homology
Function and homology information


negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / protein-arginine deiminase / histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone H3R26 arginine deiminase activity / histone H4R3 arginine deiminase activity / histone H1R54 arginine deiminase activity / histone H2AR3 arginine deiminase activity ...negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / protein-arginine deiminase / histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone H3R26 arginine deiminase activity / histone H4R3 arginine deiminase activity / histone H1R54 arginine deiminase activity / histone H2AR3 arginine deiminase activity / negative regulation of chemokine-mediated signaling pathway / 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 / 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
Protein-arginine deiminase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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_alt_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_alt_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_ptnr1_label_alt_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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,34610
Polymers78,6731
Non-polymers6739
Water13,727762
1
A: Protein-arginine deiminase type-2
hetero molecules

A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,69220
Polymers157,3462
Non-polymers1,34618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8520 Å2
ΔGint-212 kcal/mol
Surface area52850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.665, 51.549, 76.217
Angle α, β, γ (deg.)90.000, 105.760, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1375-

HOH

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Components

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


Mass: 78673.008 Da / Num. of mol.: 1
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.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
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, 2003 / 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: 1.69→40.393 Å / Num. obs: 79078 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 14.01 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.6
Reflection shellHighest resolution: 1.69 Å / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.4

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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 4N25

4n25


Resolution: 1.69→40.393 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.8742 / SU ML: 0.41 / σ(F): 1.36 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2002 2000 2.53 %
Rwork0.1675 --
obs0.1683 79077 92.8 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.039 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 82.1 Å2 / Biso mean: 20.0622 Å2 / Biso min: 4.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.1814 Å20 Å2-0.292 Å2
2--1.2075 Å20 Å2
3----0.0261 Å2
Refinement stepCycle: LAST / Resolution: 1.69→40.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5152 0 37 762 5951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115413
X-RAY DIFFRACTIONf_angle_d1.3377416
X-RAY DIFFRACTIONf_chiral_restr0.114813
X-RAY DIFFRACTIONf_plane_restr0.009938
X-RAY DIFFRACTIONf_dihedral_angle_d14.6871987
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.75010.23211110.21794298440952
1.7501-1.82020.26221700.20226515668579
1.8202-1.9030.2362070.19157997820496
1.903-2.00330.21732140.179582598473100
2.0033-2.12880.19942140.171782578471100
2.1288-2.29320.20272150.172182678482100
2.2932-2.52390.21292150.168682808495100
2.5239-2.8890.20412160.169783278543100
2.889-3.63950.18422170.161683678584100
3.6395-40.40430.17762210.14885108731100
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)
12.1196-1.12851.10231.3895-0.27173.29410.11820.15570.1334-0.1333-0.1010.127-0.24160.0357-0.0070.11820.0281-0.01960.0558-0.0460.1416-43.419913.8231-3.4688
22.6108-2.0860.36933.3721-0.56950.41910.240.195-0.2242-0.2484-0.08240.1978-0.0163-0.037-0.11070.15610.1511-0.13010.0546-0.08610.2646-55.429812.4142-9.0378
32.9133-0.30290.94280.2090.07460.5467-0.109-0.36170.29920.0401-0.0279-0.05820.0097-0.05880.06950.06750.00760.01260.11450.01320.0637-13.19044.407517.0977
42.5503-1.08950.51821.3987-0.37611.3658-0.0384-0.4488-0.20260.12080.00770.01840.0436-0.02610.00710.0538-0.02690.02890.2340.02540.054-17.8601-4.61423.2212
50.16290.18520.01420.5901-0.53220.76710.03-0.3401-0.19920.0592-0.01590.06670.0646-0.02910.02130.0832-0.01820.00870.14950.02080.074-23.7851-8.198217.5719
61.5853-0.18840.87750.30550.00020.783-0.0068-0.0868-0.14740.00160.03120.00250.0714-0.0301-0.02220.052-0.00120.02260.07030.01640.0512-8.7921-3.365516.1191
76.9268-0.1420.54985.7649-1.20282.1502-0.0886-0.4190.11280.28510.09750.0309-0.4003-0.2093-0.0070.26150.10210.0070.1876-0.02620.037820.3219-4.046739.4876
81.9994-0.906-0.00182.7522-0.03162.0675-0.0579-0.305-0.11690.14030.0063-0.0880.1545-0.06770.03440.0599-0.00730.00020.12790.05380.04157.5105-4.83824.5481
98.74821.34812.05732.289-3.32536.8582-0.2987-0.0137-0.94960.3357-0.02460.12731.28490.08330.3020.2625-0.034-0.00690.11540.04550.26211.09-15.806418.8723
102.31662.09461.8872.05032.0652.3602-0.3316-1.512-1.5241.1370.72080.31390.87860.2477-0.3840.54230.1573-0.14390.59520.17310.62719.3469-16.414928.3341
115.6472-1.5202-3.61323.27761.17434.0725-0.16560.1801-0.6444-0.07920.0287-0.06790.4673-0.39150.20960.1136-0.0493-0.02830.17050.09690.13615.3524-14.13720.2252
121.5202-0.3452-0.27550.5180.52350.69270.0370.07810.0159-0.0695-0.00540.03410.0043-0.0481-0.02140.07480.00160.00740.02510.02690.069117.5066-3.665111.0717
134.2921-1.13060.62111.0161-0.1241.4609-0.08780.03580.09610.0648-0.002-0.011-0.20460.1280.01550.0898-0.0044-0.00030.0062-0.01260.042738.07373.866322.7794
146.15335.9533-5.50367.1135-6.56776.0865-0.1101-0.01-0.3852-0.06590.0512-0.46390.36150.10510.05730.12230.0349-0.05010.1126-0.01340.121846.1952-12.422830.1228
151.14920.07090.21260.4492-0.18651.3478-0.040.0772-0.04050.00070.0568-0.02950.02940.1564-0.01140.05950.00080.00550.0214-0.02540.05934.2513-2.315217.6501
161.4848-0.3691-0.08523.7638-0.64571.2882-0.0097-0.1682-0.0639-0.04090.07320.095-0.03860.0286-0.05750.09250.0062-0.00740.0593-0.01470.024835.5385-0.867332.4095
173.4656-1.51252.5672.5583-2.23382.9751-0.00240.05960.0739-0.0636-0.044-0.08850.13160.1370.0390.06920.03170.03020.0835-0.02650.08778.93423.285520.1947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:96)A3 - 96
2X-RAY DIFFRACTION2(chain A and resid 97:112)A97 - 112
3X-RAY DIFFRACTION3(chain A and resid 113:163)A113 - 163
4X-RAY DIFFRACTION4(chain A and resid 164:193)A164 - 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 370:373)A370 - 373
10X-RAY DIFFRACTION10(chain A and resid 381:382)A381 - 382
11X-RAY DIFFRACTION11(chain A and resid 383:402)A383 - 402
12X-RAY DIFFRACTION12(chain A and resid 403:475)A403 - 475
13X-RAY DIFFRACTION13(chain A and resid 476:514)A476 - 514
14X-RAY DIFFRACTION14(chain A and resid 515:530)A515 - 530
15X-RAY DIFFRACTION15(chain A and resid 531:607)A531 - 607
16X-RAY DIFFRACTION16(chain A and resid 608:644)A608 - 644
17X-RAY DIFFRACTION17(chain A and resid 645:668)A645 - 668

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