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- PDB-4n22: Crystal structure of Protein Arginine Deiminase 2 (50 uM Ca2+) -

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Basic information

Entry
Database: PDB / ID: 4n22
TitleCrystal structure of Protein Arginine Deiminase 2 (50 uM 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 / protein-arginine deiminase / 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 ...negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / 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
ACETATE ION / Protein-arginine deiminase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.889 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 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,1418
Polymers78,6731
Non-polymers4687
Water9,152508
1
A: Protein-arginine deiminase type-2
hetero molecules

A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,28116
Polymers157,3462
Non-polymers93514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_955-x+4,y,-z1
Unit cell
Length a, b, c (Å)201.823, 51.642, 75.756
Angle α, β, γ (deg.)90.000, 105.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 515 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 49.12 %
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: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2004 / Details: vertical focusing mirrors
RadiationMonochromator: Rosenbaum-Rock double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.889→33.077 Å / Num. obs: 56093 / % possible obs: 92.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.46 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.6
Reflection shellHighest resolution: 1.889 Å / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2

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Processing

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

4n20


Resolution: 1.889→33.077 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8579 / SU ML: 0.47 / σ(F): 1.35 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 2818 5.02 %
Rwork0.1696 --
obs0.1716 56093 92.38 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.273 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 94.24 Å2 / Biso mean: 29.3479 Å2 / Biso min: 9.04 Å2
Baniso -1Baniso -2Baniso -3
1--7.6829 Å20 Å2-2.4612 Å2
2--9.6775 Å20 Å2
3----1.9945 Å2
Refinement stepCycle: LAST / Resolution: 1.889→33.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5017 0 28 508 5553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015315
X-RAY DIFFRACTIONf_angle_d1.2047259
X-RAY DIFFRACTIONf_chiral_restr0.099803
X-RAY DIFFRACTIONf_plane_restr0.007939
X-RAY DIFFRACTIONf_dihedral_angle_d12.9691926
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 (%)
1.889-1.95650.29432020.2423662386464
1.9565-2.03480.25342370.19384465470278
2.0348-2.12740.22212690.1885124539389
2.1274-2.23950.24212920.18475463575595
2.2395-2.37980.22412980.17655637593599
2.3798-2.56350.23083000.185699599999
2.5635-2.82130.21643010.17945735603699
2.8213-3.22930.20653020.168457486050100
3.2293-4.06740.17413030.147357876090100
4.0674-33.08180.18983140.158559556269100
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)
11.1326-1.16040.20560.8720.04370.56030.2052-0.0297-0.0763-0.1291-0.10320.1178-0.16430.0451-0.00250.19810.0368-0.02010.1318-0.03060.176360.40113.7518-3.3524
20.23490.056-0.02510.026-0.01160.070.22440.0899-0.3623-0.0812-0.03630.2178-0.107-0.10070.00370.2780.0964-0.11040.2002-0.06810.2703348.084712.3982-9.8867
30.39880.26240.01330.2295-0.24470.03940.039-0.11970.1956-0.0137-0.1251-0.09970.0476-0.0547-0.00340.13160.0234-0.00690.1561-0.00820.2021389.15666.983114.2485
40.810.6003-0.33770.4588-0.14250.17950.0196-0.99720.01770.1564-0.071-0.1163-0.0274-0.0819-0.00950.16940.0286-0.02490.35740.0170.1268381.4459-0.48222.7122
50.24510.3230.28240.50090.04130.22380.0386-0.2273-0.16980.052-0.03970.00550.0568-0.084300.1545-0.0216-0.00180.22050.02550.1559379.7943-8.201416.1077
60.3686-0.03010.2905-0.02380.0460.2965-0.0235-0.0865-0.0674-0.00880.0151-0.01150.0277-0.05530.00010.12120.00350.00770.14770.00490.1371395.2607-3.515616.147
70.16840.0628-0.09390.0694-0.12830.281-0.0702-0.289-0.07570.0180.03030.18360.0632-0.2620.00010.25270.03150.01940.2828-0.00630.186422.554-7.708437.3302
8-0.0046-0.01090.10590.076-0.01670.22690.0372-0.53680.1058-0.15470.0782-0.06320.0791-0.19920.00040.15810.02080.00320.21230.00720.1961410.969-4.610824.7404
90.01510.02140.01410.03190.01490.0036-0.08180.027-0.25880.01280.0768-0.09870.23730.10950.01130.38940.1265-0.03340.1701-0.01770.523415.8974-18.528622.4323
100.00940.0173-0.00720.0388-0.04010.1013-0.0083-0.00180.0255-0.0168-0.0529-0.00870.0059-0.0178-0.00030.93340.08130.16060.69260.32231.2007411.1168-22.167726.1409
110.0966-0.14010.17620.3386-0.42450.5213-0.1796-0.0667-0.75290.22380.2192-0.1116-0.1262-0.13870.07090.3151-0.04010.01610.33880.02410.4249408.9212-12.093225.8658
120.3021-0.2165-0.06310.1930.15250.13080.00110.04910.034-0.038-0.03330.06260.0288-0.047900.12260.0110.01070.09410.01210.1197421.2599-4.024711.1406
130.1523-0.1290.21770.2806-0.18440.2972-0.0485-0.0338-0.06170.0268-0.01450.0034-0.09190.0781-0.00060.13850.0109-0.00450.1344-0.00450.1214441.6233.717422.84
140.00960.0012-0.00810.0486-0.03680.0061-0.0375-0.1564-0.11910.15410.0462-0.17610.02820.1633-00.20990.0491-0.00070.20360.00740.1825449.3669-12.755130.2248
150.56390.15790.07620.11990.19430.5227-0.03370.04620.01310.00130.0388-0.0090.02040.0889-0.00010.11020.00660.01080.0823-0.01080.0968437.6606-2.01817.7601
160.6354-0.5134-0.16090.51410.03760.4142-0.0581-0.27450.00920.03570.11990.0015-0.03310.11520.09930.15520.0096-0.01710.1577-0.01290.1061439.0051-1.199732.2723
170.18380.21210.09490.2147-0.03460.0248-0.10120.14570.04280.07430.04880.04560.032-0.0160.0010.14080.03770.01280.1755-0.00820.1925412.19983.419520.526
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 113:157)A113 - 157
4X-RAY DIFFRACTION4(chain A and resid 172:193)A172 - 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 375:377)A375 - 377
11X-RAY DIFFRACTION11(chain A and resid 384:402)A384 - 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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