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- PDB-4n2e: Crystal structure of Protein Arginine Deiminase 2 (D123N, 10 mM Ca2+) -

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Basic information

Entry
Database: PDB / ID: 4n2e
TitleCrystal structure of Protein Arginine Deiminase 2 (D123N, 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
Protein-arginine deiminase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.858 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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)79,34510
Polymers78,6721
Non-polymers6739
Water10,971609
1
A: Protein-arginine deiminase type-2
hetero molecules

A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,69020
Polymers157,3442
Non-polymers1,34618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8550 Å2
ΔGint-210 kcal/mol
Surface area53340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.386, 51.917, 76.587
Angle α, β, γ (deg.)90.000, 105.630, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1245-

HOH

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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.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
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: 1.858→38.417 Å / Num. obs: 65016 / % possible obs: 99.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.79 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 15.1
Reflection shellHighest resolution: 1.858 Å / Rmerge(I) obs: 0.755 / 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 4N25

4n25


Resolution: 1.858→38.417 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8613 / SU ML: 0.46 / σ(F): 1.35 / Phase error: 21.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 3033 5 %
Rwork0.1686 --
obs0.1706 65016 99.54 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.404 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 109.28 Å2 / Biso mean: 27.6378 Å2 / Biso min: 8.57 Å2
Baniso -1Baniso -2Baniso -3
1--8.2067 Å20 Å2-1.2026 Å2
2--10.583 Å20 Å2
3----2.3763 Å2
Refinement stepCycle: LAST / Resolution: 1.858→38.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5149 0 37 609 5795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115403
X-RAY DIFFRACTIONf_angle_d1.3167401
X-RAY DIFFRACTIONf_chiral_restr0.108812
X-RAY DIFFRACTIONf_plane_restr0.007935
X-RAY DIFFRACTIONf_dihedral_angle_d14.441980
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 (%)
1.858-1.9240.28323190.24586031635098
1.924-2.0010.27343200.20596093641399
2.001-2.09210.23443240.18296134645899
2.0921-2.20240.2213250.175961596484100
2.2024-2.34030.22153230.176461466469100
2.3403-2.5210.20383230.167261436466100
2.521-2.77460.23973270.177262106537100
2.7746-3.1760.22693280.174262346562100
3.176-4.00070.18883290.153862466575100
4.0007-38.42560.16193350.145563676702100
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)
13.225-1.57461.2331.8229-0.81363.68850.10870.10960.1002-0.128-0.0910.111-0.2456-0.0003-0.03330.15110.0178-0.01310.092-0.05720.1785-43.530413.841-3.5212
25.1521-2.4091.26084.0357-0.53310.84740.53030.3407-0.5705-0.424-0.1240.47040.1595-0.1295-0.31420.25220.1073-0.10810.1445-0.09410.3238-55.588912.4856-9.1038
33.3402-0.42550.9740.5825-0.08670.8378-0.1068-0.37120.27510.0574-0.0355-0.1319-0.0026-0.08770.11510.12030.00080.00430.16010.00190.1128-13.19534.347617.1779
43.1993-1.49481.0321.6381-0.52091.6587-0.0085-0.5493-0.29560.11460.09090.08820.0435-0.1164-0.06910.1331-0.03860.0170.29090.04210.1165-17.8734-4.743623.2997
50.62290.19890.14260.8195-0.570.78850.0545-0.3683-0.19950.0545-0.01270.04870.0418-0.0681-0.02050.1533-0.0265-0.0050.21990.02570.1436-23.7931-8.281417.5584
62.2476-0.11511.19380.17830.06571.14820.0101-0.0566-0.18120.02050.0288-0.00380.0974-0.0272-0.0440.11080.00170.02050.0860.01780.1104-8.7838-3.467516.2024
78.4989-0.8080.76346.5422-1.60663.0447-0.2125-0.55730.11080.44780.18790.0649-0.4663-0.16480.0210.31290.07480.00480.2315-0.01370.104520.4397-4.189939.6864
83.9062-1.97921.15373.7616-0.8732.29010.0537-0.5382-0.086-0.02250.0083-0.14680.10920.0047-0.04420.1257-0.01780.00710.18130.04950.09947.6006-4.958724.6814
96.31582.32422.43083.5505-2.72545.7978-0.31410.1462-0.9141-0.1003-0.12840.14511.4172-0.13520.38870.341-0.04520.00940.18980.01680.424311.2084-15.931118.9627
107.2964-3.29162.62112.69630.23232.5937-0.4337-0.7384-0.57580.65670.65370.5196-0.0083-0.2028-0.20820.90260.2587-0.37780.75230.14240.88589.3879-16.575928.37
115.5739-1.1088-2.11034.02791.06353.6415-0.00450.1425-0.7934-0.14720.1136-0.21220.4206-0.3171-0.01870.1834-0.0686-0.06440.23430.07970.2125.4249-14.263620.326
122.3102-0.5304-0.42270.30760.51671.14790.03140.1185-0.0197-0.0939-0.01040.06680.0108-0.0577-0.00990.1407-0.0001-0.00040.09550.02460.135617.6036-3.741411.1273
133.9221-1.04520.88211.1788-0.18191.9836-0.09190.07680.15280.0786-0.0114-0.0121-0.2250.16210.05940.1399-0.02380.00440.0532-0.00230.097838.23163.840822.8997
144.81384.6781-3.55286.2062-4.81493.7348-0.1274-0.0617-0.5484-0.0157-0.0049-0.60410.30520.18120.05560.19180.0431-0.0420.1681-0.00630.206946.492-12.507130.2301
151.57540.06720.49970.6209-0.29312.0305-0.01640.1442-0.0697-0.01060.0563-0.04010.04730.1736-0.03070.0938-0.00980.00860.0658-0.02620.112334.2469-2.293617.8059
161.9134-0.742-0.02273.5807-0.75941.5741-0.0145-0.2516-0.0321-0.01390.08670.0606-0.00840.0302-0.06150.16770.0089-0.01930.1457-0.01050.096535.7363-0.937132.5803
172.9604-0.58541.96652.0504-1.94823.1120.04270.16070.0442-0.08-0.1955-0.12420.23340.24410.13890.13610.04990.02580.1365-0.01360.14389.00963.185920.3281
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 381:382)A381 - 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 645:668)A645 - 668

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