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- PDB-4n2g: Crystal structure of Protein Arginine Deiminase 2 (D169A, 10 mM Ca2+) -

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Basic information

Entry
Database: PDB / ID: 4n2g
TitleCrystal structure of Protein Arginine Deiminase 2 (D169A, 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 / 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
ACETATE ION / Protein-arginine deiminase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)79,53112
Polymers78,6291
Non-polymers90211
Water7,656425
1
A: Protein-arginine deiminase type-2
hetero molecules

A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,06324
Polymers157,2582
Non-polymers1,80522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area9570 Å2
ΔGint-223 kcal/mol
Surface area52560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.450, 50.940, 75.940
Angle α, β, γ (deg.)90.000, 105.980, 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: 78629.000 Da / Num. of mol.: 1 / Mutation: D169A
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, 436 molecules

#2: Chemical
ChemComp-MPD / (4S)-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.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 425 / 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2010 / 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: 1.85→37.782 Å / Num. obs: 64573 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 26.14 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.6
Reflection shellHighest resolution: 1.85 Å / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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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: 1.85→37.782 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.8483 / SU ML: 0.49 / σ(F): 1.34 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2161 3269 5.06 %
Rwork0.1785 --
obs0.1804 64573 99.94 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.885 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 110.55 Å2 / Biso mean: 37.0827 Å2 / Biso min: 13.41 Å2
Baniso -1Baniso -2Baniso -3
1--4.9856 Å20 Å2-1.9049 Å2
2--10.1354 Å20 Å2
3----5.1497 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5143 0 54 425 5622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015365
X-RAY DIFFRACTIONf_angle_d1.2497333
X-RAY DIFFRACTIONf_chiral_restr0.103810
X-RAY DIFFRACTIONf_plane_restr0.007928
X-RAY DIFFRACTIONf_dihedral_angle_d14.5761945
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.91610.26783080.245961026410
1.9161-1.99280.27153030.213461176420
1.9928-2.08350.23163080.191560906398
2.0835-2.19340.23353430.178360956438
2.1934-2.33080.2233440.182660776421
2.3308-2.51070.2272940.184461316425
2.5107-2.76330.23363310.191261186449
2.7633-3.1630.2193530.181861326485
3.163-3.98430.19033500.161561436493
3.9843-37.78940.20583350.168262996634
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)
14.6484-1.90531.36143.17460.81885.53840.1969-0.14620.2051-0.6067-0.02850.1027-0.71120.0648-0.14460.37960.01930.01910.187-0.06010.2458-64.213613.006269.5763
22.9185-1.61351.8633.4749-0.84191.24710.63750.1283-0.0812-1.11-0.49960.86860.0805-0.4126-0.22290.53130.1744-0.19720.3984-0.10330.4752-76.451111.72763.4674
34.9968-0.57241.79350.2515-0.0121.1504-0.1167-0.70990.240.10910.04540.0437-0.0365-0.35940.02630.18120.02390.01890.4182-0.01110.1361-34.34383.493290.4241
44.3802-0.86610.5241.0820.32951.3298-0.0627-1.3374-1.02120.88860.2699-0.30370.1435-0.753-0.13820.158-0.07020.13720.82450.1275-0.0232-38.1635-4.987296.5108
50.10270.3138-0.60260.8644-0.87611.3039-0.0059-0.3447-0.23010.13720.06890.1645-0.0643-0.1094-0.01190.2252-0.04830.00680.5240.02980.2157-45.0105-8.714390.4118
64.1327-0.19252.08440.14460.11831.51580.0023-0.1235-0.26070.01650.05370.04380.0587-0.2046-0.08240.1889-0.01470.03050.30230.0370.1628-29.0496-4.270189.8007
78.1160.44561.10368.5399-5.19916.0622-0.3608-0.45860.17690.73630.37110.0457-0.6012-0.16580.06550.36560.084-0.00260.3062-0.03960.1194-0.6207-4.4514112.67
88.6895-5.99741.16447.8632-1.36565.2073-0.0882-0.67940.04470.09760.1193-0.28710.3535-0.27290.02430.1786-0.07170.00240.26780.03630.1272-13.7139-5.321297.9085
90.20410.21550.68336.141-0.31092.9797-0.4988-0.0851-2.60320.9368-0.2782-0.09582.5163-0.28030.61360.5572-0.05530.04180.31630.04620.6623-9.2688-18.617391.8715
103.6104-2.9615-5.95548.92355.14749.825-1.264-1.918-1.51471.70681.1857-1.01031.54911.6257-0.02930.59920.0978-0.21530.60050.04040.8408-8.2859-22.621395.4469
116.4603-1.821-3.36182.91332.24176.38480.0903-0.2436-0.73230.16510.113-0.00240.616-0.3164-0.08230.2511-0.0609-0.0970.32080.11570.3154-15.3467-14.360293.8749
124.4873-1.7026-0.07851.18860.18061.44450.10420.3151-0.0881-0.1568-0.05840.04540.012-0.1118-0.03750.1828-0.02370.0060.1550.02370.147-3.3073-4.464984.3256
137.3317-1.72631.67151.4572-0.64172.4441-0.13230.03760.34710.10910.0168-0.1356-0.20930.10080.05520.1691-0.03350.00250.0507-0.00040.145917.05593.611895.7826
146.15317.624-6.30799.3152-7.79776.3163-0.0234-0.2398-0.49320.0982-0.0498-0.77580.23170.59190.06970.20210.0246-0.00940.2580.00390.236725.8203-12.8613103.058
152.533-0.36560.38930.7832-0.17612.0285-0.02620.211-0.1034-0.05130.0284-0.04360.06430.11560.0120.1536-0.02770.02050.0807-0.01150.15813.2427-2.76390.64
162.9619-1.4603-0.07398.1723-1.18162.6602-0.051-0.2865-0.21830.02920.07620.20550.10270.0738-0.03920.1393-0.003-0.01390.13160.00320.111814.8445-1.3695105.4299
175.2037-1.74422.59574.608-2.16213.87280.04130.49070.0612-0.1791-0.2127-0.14610.10120.44260.15240.12530.03050.05930.2399-0.01250.1598-11.86072.932994.4851
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 370:374)A370 - 374
10X-RAY DIFFRACTION10(chain A and resid 375:382)A375 - 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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