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- PDB-4n2d: Crystal structure of Protein Arginine Deiminase 2 (D123N, 0 mM Ca2+) -

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Basic information

Entry
Database: PDB / ID: 4n2d
TitleCrystal structure of Protein Arginine Deiminase 2 (D123N, 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
Protein-arginine deiminase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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_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_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)79,1076
Polymers78,6721
Non-polymers4355
Water4,990277
1
A: Protein-arginine deiminase type-2
hetero molecules

A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,21312
Polymers157,3442
Non-polymers86910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area7560 Å2
ΔGint-132 kcal/mol
Surface area51120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.190, 51.820, 75.895
Angle α, β, γ (deg.)90.000, 105.660, 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: 78672.016 Da / Num. of mol.: 1 / Mutation: D123N
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
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: 2→36.248 Å / Num. obs: 52659 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.86 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.7
Reflection shellHighest resolution: 2 Å / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.5

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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: 2→36.248 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.837 / SU ML: 0.68 / σ(F): 1.35 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 2627 4.99 %
Rwork0.1779 --
obs0.1801 52659 88 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.848 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso max: 109.17 Å2 / Biso mean: 31.8151 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.2593 Å20 Å2-0.2286 Å2
2--0.7909 Å20 Å2
3---0.4684 Å2
Refinement stepCycle: LAST / Resolution: 2→36.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4941 0 26 277 5244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015197
X-RAY DIFFRACTIONf_angle_d1.3127095
X-RAY DIFFRACTIONf_chiral_restr0.101791
X-RAY DIFFRACTIONf_plane_restr0.007910
X-RAY DIFFRACTIONf_dihedral_angle_d13.1371874
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 (%)
2-2.07140.24481220.18922258238024
2.0714-2.15440.24012070.20113993420042
2.1544-2.25240.25812430.2074651489449
2.2524-2.37110.23542520.20674844509651
2.3711-2.51970.27652550.22134838509351
2.5197-2.71420.27632580.2214893515151
2.7142-2.98720.23032560.21414888514451
2.9872-3.41910.25082580.20234912517052
3.4191-4.30660.20563290.15386110643964
4.3066-36.25380.19334470.14858645909291
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)
14.3599-2.30022.05992.4891-0.71585.42610.15540.1190.0546-0.172-0.07250.1076-0.2736-0.0361-0.06070.13640.0055-0.0070.0574-0.04710.1576158.9499.1831-3.2931
24.9781-1.04280.86024.0001-0.00441.67640.51920.1029-0.3237-0.1478-0.22030.7245-0.1952-0.3601-0.23440.2810.1461-0.17180.1557-0.10950.3525146.83457.6991-9.0487
38.2131-0.65431.97720.33230.15470.6276-0.0242-0.11150.7038-0.0446-0.046-0.13370.0059-0.06650.07070.17710.01690.00070.1708-0.01410.2033187.50892.846314.0887
43.32191.8915-0.4821.91080.95581.75550.3192-2.0715-0.78791.0909-0.3043-0.57370.3657-0.02690.01180.19460.12870.08420.55440.0781-0.0174180.0231-5.180622.6723
52.7650.18090.64111.5855-0.09831.3448-0.0084-0.8855-0.76880.27150.06070.06080.0943-0.0753-0.00720.2174-0.0197-0.00630.30650.07160.2076178.2466-12.632315.7951
63.7834-0.24281.75790.02690.09971.25150.0137-0.1341-0.2310.01770.04760.02210.0945-0.0613-0.07560.1691-0.01380.01760.13170.0290.1518193.6345-7.95716.2672
76.74850.17880.79165.6150.78986.5239-0.0603-0.6081-0.39040.2829-0.02150.50720.3571-0.45770.04950.23280.0630.02840.24360.04670.0977221.1317-12.041737.2343
87.2058-6.49814.61096.8741-4.01274.31480.0941-0.8545-0.1547-0.24430.07720.01680.257-0.2849-0.09960.1389-0.01770.00790.2250.02030.2548209.5103-9.180924.7017
91.9757-1.1463.51131.7328-3.37597.9202-0.79150.0412-1.59040.38050.7819-0.29741.47140.8869-0.04960.72620.2580.00720.5526-0.1290.6764214.3959-23.05722.4622
100.70150.3546-0.04410.54240.83972.04850.06870.07970.1575-0.2224-0.20090.1393-0.4053-0.08720.11560.87190.22070.19840.56540.42521.7933209.755-25.88624.7352
113.9388-1.87840.57581.4797-0.41520.1042-0.9061-0.8416-1.51731.0660.42490.96280.5771-0.59890.25770.3995-0.01630.19220.58780.22770.5348206.6391-15.335726.1909
123.6816-1.5023-0.34850.93470.35730.82030.02560.1656-0.0353-0.0774-0.05180.0773-0.0464-0.04950.0440.173-0.00270.00590.12640.03030.1308219.8141-8.653611.1584
136.8737-1.58222.10191.2812-0.75252.1618-0.02760.02720.16780.06320.0034-0.0528-0.21320.1216-0.02490.15810.0005-0.00660.0975-0.00240.0985240.2375-0.789422.7667
145.17187.0015-6.13039.3943-8.25747.2869-0.1215-0.3166-0.5035-0.0120.0577-0.36750.40070.11370.1230.21820.0712-0.03770.2293-0.01210.1754247.9575-17.27930.2821
151.9106-0.00960.19070.90930.09991.941-0.04480.0708-0.03060.00380.0791-0.02160.07750.1045-0.01440.1143-0.02250.00520.0846-0.00690.1042236.3506-6.800117.7475
162.1426-1.2379-0.03235.8763-1.15322.1638-0.1145-0.37930.01340.12370.23790.1053-0.0417-0.0023-0.09140.15260.0082-0.01270.1921-0.01590.0649237.5697-5.701532.2826
174.2836-2.12343.58433.4303-2.77064.0553-0.00240.15430.4532-0.2416-0.1938-0.27780.320.01870.17770.16630.01310.04010.18090.0140.16210.5614-0.816120.1338
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 113:156)A113 - 156
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 375:376)A375 - 376
11X-RAY DIFFRACTION11(chain A and resid 386:402)A386 - 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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