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- PDB-4n26: Crystal structure of Protein Arginine Deiminase 2 (500 uM Ca2+) -

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Basic information

Entry
Database: PDB / ID: 4n26
TitleCrystal structure of Protein Arginine Deiminase 2 (500 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: 1.943 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.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)79,28710
Polymers78,6731
Non-polymers6149
Water9,440524
1
A: Protein-arginine deiminase type-2
hetero molecules

A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,57420
Polymers157,3462
Non-polymers1,22818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area8190 Å2
ΔGint-185 kcal/mol
Surface area52980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.278, 51.675, 76.099
Angle α, β, γ (deg.)90.000, 105.550, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1252-

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.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 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: 1.94→33.995 Å / Num. obs: 52719 / % possible obs: 93.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.97 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.7
Reflection shellHighest resolution: 1.94 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.1

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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: 1.943→33.995 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.851 / SU ML: 0.54 / σ(F): 1.35 / Phase error: 22.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2223 2619 4.97 %
Rwork0.1695 --
obs0.1721 52719 93.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.292 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 115.03 Å2 / Biso mean: 29.7334 Å2 / Biso min: 8.99 Å2
Baniso -1Baniso -2Baniso -3
1--6.8867 Å20 Å2-3.1413 Å2
2--8.3906 Å20 Å2
3----1.5039 Å2
Refinement stepCycle: LAST / Resolution: 1.943→33.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5168 0 33 524 5725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015405
X-RAY DIFFRACTIONf_angle_d1.2437394
X-RAY DIFFRACTIONf_chiral_restr0.099810
X-RAY DIFFRACTIONf_plane_restr0.007937
X-RAY DIFFRACTIONf_dihedral_angle_d13.8241978
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 (%)
1.943-2.01260.30922090.2423788399771
2.0126-2.09320.27092270.19684539476685
2.0932-2.18850.25862530.18654969522293
2.1885-2.30380.22782720.17775126539897
2.3038-2.44810.2612750.1765204547998
2.4481-2.63710.24022670.17745190545798
2.6371-2.90230.23912750.17745246552198
2.9023-3.3220.23172730.17095243551698
3.322-4.18410.18762790.14635331561099
4.1841-34.00010.192890.15745464575399
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)
10.7516-0.653-0.10170.7505-0.19440.57680.15850.0495-0.0525-0.0682-0.07810.1082-0.10180.0925-0.0190.17890.0436-0.01320.1295-0.04080.1864138.575113.979669.8278
20.0860.0374-0.01190.0195-0.06970.07520.25540.083-0.2961-0.0732-0.19870.2261-0.0676-0.02210.00460.20260.1988-0.1307-0.0418-0.13230.3074126.208512.718863.4495
30.6545-0.01150.13680.6295-0.33430.4704-0.0452-0.22250.12190.0417-0.1199-0.1557-0.0021-0.0031-0.23180.10950.0046-0.00380.15220.00880.129168.58794.41490.3926
40.32080.3155-0.01110.2572-0.06240.11570.0762-0.4277-0.19860.0785-0.0491-0.07020.01540.0832-0.00850.11280.0136-0.01190.32140.03420.1282164.7677-4.578296.7876
50.03060.09440.02670.3606-0.01620.01650.0709-0.3764-0.28480.0187-0.04110.02330.0454-0.0960.00540.1612-0.0348-0.00010.26720.03370.1433158.2931-8.110390.716
60.1149-0.02950.2585-0.01530.03840.2057-0.0244-0.1022-0.0552-0.01250.0067-0.01750.0354-0.0181-0.00020.08740.0070.00850.14070.01490.1109173.1169-3.183489.4428
70.145-0.0137-0.02560.052-0.08640.0512-0.086-0.1309-0.25190.09820.17540.1988-0.0901-0.22710.00020.24060.04610.02150.2455-0.00730.2068201.6535-4.9982111.8976
8-0.01060.08220.11210.1084-0.01020.09020.1718-0.24650.1955-0.0523-0.1461-0.13720.0644-0.1491-0.00190.1477-0.0201-0.00840.24120.05320.18189.0983-4.452697.9699
90.0049-0.0009-0.01470.04180.03270.0407-0.11340.0021-0.0109-0.129-0.0235-0.02030.1996-0.0618-0.00010.410.0314-0.12040.3401-0.04570.5777192.9685-15.646292.2044
100.00060.00160.00010.0011-0.00130.0003-0.0762-0.0394-0.00620.0094-0.0923-0.015-0.0162-0.05140.00020.5430.0357-0.14690.3896-0.22890.5892192.0745-20.272196.6353
110.04950.0341-0.01950.01760.06930.06050.12710.0726-0.2630.03450.2546-0.04190.1799-0.08080.00830.2198-0.0037-0.00370.46990.13380.4805186.8152-13.002595.6856
120.2932-0.0406-0.15730.0659-0.04750.19250.01120.03250.0188-0.00480.00340.01390.0143-0.0341-00.13270.00270.00720.09080.01380.1261199.4041-3.498484.3991
130.11280.04140.17970.0978-0.06890.2956-0.0699-0.0059-0.06090.01110.01690.0255-0.1030.072400.1480.0077-0.01440.1438-0.01160.135219.95074.005396.1166
140.003-0.0205-0.00290.0133-0.015-0.00750.0161-0.1231-0.10220.01360.0488-0.19390.10530.135900.18240.0228-0.01070.16840.00630.2237228.1081-12.2202103.5934
150.26680.14460.088-0.00680.16580.304-0.03220.052-0.00450.01240.0591-0.00750.0260.05940.00230.11580.00980.00910.0907-0.01290.0999216.0069-2.1490.9074
160.3327-0.1059-0.03910.1569-0.02260.2367-0.0302-0.18020.01980.04190.0694-0.0376-0.01310.05170.01960.15910.0126-0.00930.1068-0.00630.093217.4336-0.6463105.7527
170.1590.14530.05070.0118-0.0446-0.0449-0.00590.10840.0475-0.0253-0.0825-0.05630.09510.033900.14760.0453-0.00150.16070.01360.1708190.61083.838493.7903
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 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 645:667)A645 - 667

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