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- PDB-4n2l: Crystal structure of Protein Arginine Deiminase 2 (Q350A, 10 mM Ca2+) -

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Basic information

Entry
Database: PDB / ID: 4n2l
TitleCrystal structure of Protein Arginine Deiminase 2 (Q350A, 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 / histone H3R26 arginine deiminase activity / negative regulation of chemokine-mediated signaling pathway / protein-arginine deiminase / protein-arginine deiminase activity / intracellular estrogen receptor signaling pathway / Chromatin modifying enzymes / transcription initiation-coupled chromatin remodeling / substantia nigra development ...negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / negative regulation of chemokine-mediated signaling pathway / protein-arginine deiminase / protein-arginine deiminase activity / intracellular estrogen receptor signaling pathway / Chromatin modifying enzymes / transcription initiation-coupled chromatin remodeling / substantia nigra development / 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
ACETATE ION / Protein-arginine deiminase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 5, 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.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.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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,70216
Polymers78,6161
Non-polymers1,08615
Water7,584421
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A: Protein-arginine deiminase type-2
hetero molecules

A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,40532
Polymers157,2322
Non-polymers2,17330
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11390 Å2
ΔGint-241 kcal/mol
Surface area52720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.380, 51.100, 76.180
Angle α, β, γ (deg.)90.000, 105.600, 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: 78615.953 Da / Num. of mol.: 1 / Mutation: Q350A
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 / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / 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: Chemical
ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.42 Å3/Da / Density % sol: 49.28 %

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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 / 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: 2.1→40.242 Å / Num. obs: 44320 / Biso Wilson estimate: 23.73 Å2
Reflection shellHighest resolution: 2.1 Å

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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: 2.1→40.242 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8419 / SU ML: 0.56 / σ(F): 1.36 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2153 2237 5.05 %
Rwork0.1652 --
obs0.1678 44320 99.74 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.206 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 104.67 Å2 / Biso mean: 32.8102 Å2 / Biso min: 10.58 Å2
Baniso -1Baniso -2Baniso -3
1--9.8704 Å20 Å20.0678 Å2
2--13.779 Å20 Å2
3----3.9086 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5182 0 65 421 5668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115423
X-RAY DIFFRACTIONf_angle_d1.2197414
X-RAY DIFFRACTIONf_chiral_restr0.101811
X-RAY DIFFRACTIONf_plane_restr0.007939
X-RAY DIFFRACTIONf_dihedral_angle_d15.1321972
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 (%)
2.1-2.17510.28252190.21224147436699
2.1751-2.26210.23512270.18764141436899
2.2621-2.36510.2792030.178542054408100
2.3651-2.48970.26932370.185841644401100
2.4897-2.64570.25491950.185741964391100
2.6457-2.84990.26212100.183842204430100
2.8499-3.13660.25182200.168541974417100
3.1366-3.59030.18452380.153542214459100
3.5903-4.52240.16562510.130942384489100
4.5224-40.24920.18912370.162443544591100
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)
13.4295-1.51991.48882.2207-0.3644.33890.1950.04360.1058-0.1749-0.0970.1642-0.2184-0.0452-0.10980.14520.02490.00850.0974-0.0510.1538-43.346112.6377-3.5561
29.5569-1.49121.75265.50230.63890.71840.59430.4828-0.1593-0.7444-0.24860.77490.3496-0.0769-0.38680.23270.0516-0.0820.2027-0.07860.2838-55.519911.3145-9.7131
33.2432-0.67041.21250.5217-0.01361.1894-0.0702-0.75530.19750.1024-0.0263-0.05430.0111-0.1490.05420.15610.0040.00990.27420.02150.1432-13.37643.067217.2199
42.4623-1.04281.05841.233-0.39122.0684-0.2089-0.8521-0.35060.20420.2260.0207-0.0781-0.01030.01870.1494-0.01860.02190.51780.09840.2075-17.182-5.988423.5212
50.54320.2185-0.14651.2294-1.07481.207-0.0127-0.6018-0.34350.0838-0.01740.10110.0363-0.04090.03950.1706-0.02690.00110.32550.02760.2087-23.718-9.587917.5385
63.7015-0.16471.63520.05020.13631.0881-0.0135-0.0927-0.25660.01430.07360.00080.0693-0.064-0.06180.1552-0.00950.0240.20840.030.1508-8.1708-4.779216.6749
78.5219-0.16370.52553.611-0.75372.8983-0.2426-0.8680.06990.28510.31650.0408-0.5897-0.42590.00210.34780.09260.02690.3041-0.02490.093120.0878-4.971839.7549
81.14560.64860.46942.9004-0.43873.9409-0.0373-0.58950.04910.07270.0271-0.23830.29120.11120.04220.143-0.02640.00580.34790.06290.1036.3312-5.705724.7063
92.0013-1.8758-2.88061.50310.48463.0302-0.664-0.2764-1.81380.2813-0.12750.13591.9741-0.16520.72210.48590.00230.10430.42430.20360.486111.1199-18.801118.9874
100.71130.9557-1.34111.3879-2.06673.1977-0.530.2522-1.24060.8522-0.73851.56311.5199-1.11941.20090.5232-0.15460.15690.5151-0.15181.007410.2699-21.183324.0015
113.7822-0.6241-2.7762.71611.76083.45150.0621-0.3575-0.73850.07250.2476-0.23720.3345-0.2907-0.0780.214-0.0595-0.10160.46530.16760.28945.4543-15.070621.0951
123.6779-1.396-0.19340.93670.34931.53940.0190.1924-0.0572-0.0762-0.05060.04740.048-0.05450.04530.1421-0.02250.00130.12860.0460.135417.6316-4.989911.2429
136.9135-2.46411.4950.892-0.58622.3943-0.0177-0.05730.38820.0885-0.0083-0.088-0.18020.08480.01930.1655-0.04430.00980.06550.00430.187138.17262.762922.9448
148.21268.0619-7.65478.8097-8.55768.3121-0.1531-0.5825-0.5683-0.0948-0.1628-0.64010.24930.71920.26990.16030.0357-0.03040.22-0.04480.197946.7475-13.522130.2116
152.320.03690.27170.2023-0.05872.2095-0.03570.1569-0.0377-0.00310.0545-0.00540.05210.0379-0.01970.1384-0.02880.01440.0646-0.01060.138933.7906-3.194717.9607
162.6364-0.4517-0.29615.8513-0.58432.4748-0.1227-0.3311-0.0660.12090.11270.08930.04220.08510.00070.14310.00090.00920.1215-0.00420.071735.6967-2.02132.5769
174.6918-1.55192.87213.5374-2.97714.09680.1030.30420.0746-0.1782-0.2225-0.02430.22910.47730.08240.16560.02020.05950.247-0.04260.16099.2611.993920.5647
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 113:163)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 370:374)A370 - 374
10X-RAY DIFFRACTION10(chain A and resid 378:382)A378 - 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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