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- PDB-4n2k: Crystal structure of Protein Arginine Deiminase 2 (Q350A, 0 mM Ca2+) -

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Basic information

Entry
Database: PDB / ID: 4n2k
TitleCrystal structure of Protein Arginine Deiminase 2 (Q350A, 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 / histone H3R26 arginine deiminase activity / negative regulation of chemokine-mediated signaling pathway / protein-arginine deiminase / protein-arginine deiminase activity / 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 / 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 / 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: 1.57 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)79,1437
Polymers78,6161
Non-polymers5276
Water12,809711
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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)158,28514
Polymers157,2322
Non-polymers1,05412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area8170 Å2
ΔGint-133 kcal/mol
Surface area52820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.242, 51.940, 75.969
Angle α, β, γ (deg.)90.000, 105.310, 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


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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
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: Jun 28, 2013 / 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: 1.57→40.582 Å / Num. obs: 103006 / % possible obs: 96.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.22 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 26.8
Reflection shellHighest resolution: 1.57 Å / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2

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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: 1.57→40.582 Å / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.8712 / SU ML: 0.42 / σ(F): 1.36 / Phase error: 20.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 4877 5.01 %
Rwork0.1779 --
obs0.1794 103006 96.69 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.077 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 87.21 Å2 / Biso mean: 26.3185 Å2 / Biso min: 7.79 Å2
Baniso -1Baniso -2Baniso -3
1--5.0304 Å20 Å2-1.6626 Å2
2--5.6937 Å20 Å2
3----0.6633 Å2
Refinement stepCycle: LAST / Resolution: 1.57→40.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5000 0 32 711 5743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075320
X-RAY DIFFRACTIONf_angle_d1.2447255
X-RAY DIFFRACTIONf_chiral_restr0.105802
X-RAY DIFFRACTIONf_plane_restr0.008936
X-RAY DIFFRACTIONf_dihedral_angle_d12.7961954
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 (%)
1.57-1.62610.30344940.27189399989393
1.6261-1.69120.264990.230795971009696
1.6912-1.76820.25415120.204497151022796
1.7682-1.86140.21545140.181696471016196
1.8614-1.9780.21335160.175297311024797
1.978-2.13080.19945100.171998051031597
2.1308-2.34520.20485230.178798511037497
2.3452-2.68450.22075230.181899121043598
2.6845-3.38190.20745310.1773100011053298
3.3819-40.59520.18525390.1609101871072698
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)
12.8315-1.49091.18421.7907-0.16574.30680.18830.12440.0034-0.2426-0.07380.0984-0.17350.0763-0.09930.1380.0114-0.0070.074-0.03460.1298138.838813.617469.9607
26.4759-1.63792.31153.3699-0.68751.92370.28850.3226-0.2169-0.4188-0.13020.5003-0.0715-0.2156-0.20240.23940.1025-0.11120.1872-0.07840.2546126.660412.441363.7965
34.9859-0.16561.53710.1952-0.22710.5352-0.1019-0.23120.5512-0.0133-0.0618-0.0993-0.0139-0.06970.15290.13240.0179-0.00680.1669-0.01250.1904167.58797.380487.3399
43.35390.08310.24791.8132-0.42081.8484-0.0932-1.4224-0.28490.41170.0192-0.17930.211-0.12670.04750.19980.0255-0.00110.46060.04480.1138159.3802-0.868795.8926
50.96080.48670.21131.08890.09811.03060.006-0.7523-0.40220.2034-0.00480.03120.1842-0.05850.06210.1597-0.01190.01890.26550.05150.1408157.911-8.05689.6245
62.5902-0.15821.46180.00180.01211.06070.0235-0.0618-0.13150.00020.02350.01520.082-0.0351-0.05290.11540.00230.01140.1260.00910.1404173.8042-3.495389.5111
75.8816-0.05170.67534.78250.03935.13370.0101-0.2989-0.23130.02030.04250.40140.0828-0.6097-0.03410.18330.03220.01710.23480.01870.1393201.3389-7.633110.8756
86.8119-3.39211.17185.3616-1.64032.9934-0.3222-0.73770.05820.39670.3678-0.1416-0.0031-0.26570.00350.11290.02990.00280.1901-0.00660.1153189.0317-4.190498.1469
94.5360.00182.29845.206-0.7522.3293-0.199-0.3813-1.57160.19270.48320.61721.40080.6184-0.32210.76040.11320.1250.3060.00720.6534194.2755-18.835195.9777
103.6619-2.4221-1.92292.30280.6812.3979-0.7838-1.1198-1.09220.78270.3340.22580.41220.09160.3950.3127-0.01050.06380.51170.10120.3892186.9172-10.8613100.9767
112.4226-0.938-0.57040.98840.45360.7621-0.00420.0950.0045-0.0947-0.0180.06840.0229-0.08930.02850.1295-0.00040.00010.11780.0240.1143199.8367-3.816784.4552
124.3688-0.86961.1770.6352-0.30611.6764-0.11690.04550.17210.03420.0261-0.0234-0.17750.06820.0390.1378-0.00280.00040.08080.00020.096220.16433.921196.0709
135.06584.2783-4.03465.0746-4.44963.9476-0.1249-0.2664-0.5655-0.1008-0.1272-0.41690.36760.42020.1780.1460.0423-0.02030.14220.00560.1338228.389-12.9622103.7523
141.2889-0.03860.25440.3912-0.02591.2579-0.03630.1113-0.0205-0.01030.0303-0.01750.04790.11180.00550.0953-0.00240.00810.0772-0.01040.0847216.518-2.433791.2757
151.5152-0.51470.03284.5265-0.48091.3082-0.039-0.20250.04250.06070.06310.0898-0.06310.0247-0.02480.11970.017-0.00060.1382-0.01560.0597217.623-0.9124105.7422
163.1557-1.39912.24992.1572-2.172.4945-0.06790.12810.16120.0222-0.0653-0.02850.13880.09170.13080.1430.04680.01920.1624-0.02770.1736190.64223.700393.4542
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 370:375)A370 - 375
10X-RAY DIFFRACTION10(chain A and resid 384:402)A384 - 402
11X-RAY DIFFRACTION11(chain A and resid 403:475)A403 - 475
12X-RAY DIFFRACTION12(chain A and resid 476:514)A476 - 514
13X-RAY DIFFRACTION13(chain A and resid 515:530)A515 - 530
14X-RAY DIFFRACTION14(chain A and resid 531:607)A531 - 607
15X-RAY DIFFRACTION15(chain A and resid 608:644)A608 - 644
16X-RAY DIFFRACTION16(chain A and resid 645:668)A645 - 668

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