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- PDB-4n2h: Crystal structure of Protein Arginine Deiminase 2 (D177A, 0 mM Ca2+) -

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Basic information

Entry
Database: PDB / ID: 4n2h
TitleCrystal structure of Protein Arginine Deiminase 2 (D177A, 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 / 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
Protein-arginine deiminase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.808 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.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

Downloads & links

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Assembly

Deposited unit
A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0646
Polymers78,6291
Non-polymers4355
Water12,160675
1
A: Protein-arginine deiminase type-2
hetero molecules

A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,12712
Polymers157,2582
Non-polymers86910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area7470 Å2
ΔGint-129 kcal/mol
Surface area53200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.312, 52.035, 76.072
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: 78629.000 Da / Num. of mol.: 1 / Mutation: D177A
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.: 675 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
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: 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: 1.8→40.633 Å / Num. obs: 69484 / % possible obs: 99.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.08 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.6
Reflection shellHighest resolution: 1.8 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / % 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 4N20

4n20


Resolution: 1.808→40.633 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.8721 / SU ML: 0.48 / σ(F): 1.36 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2109 3259 5 %
Rwork0.1722 --
obs0.1742 69484 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.829 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 94.73 Å2 / Biso mean: 27.9177 Å2 / Biso min: 8.17 Å2
Baniso -1Baniso -2Baniso -3
1--5.0744 Å20 Å2-2.3117 Å2
2--6.0272 Å20 Å2
3----0.9528 Å2
Refinement stepCycle: LAST / Resolution: 1.808→40.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5033 0 26 675 5734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085300
X-RAY DIFFRACTIONf_angle_d1.2637232
X-RAY DIFFRACTIONf_chiral_restr0.109798
X-RAY DIFFRACTIONf_plane_restr0.007927
X-RAY DIFFRACTIONf_dihedral_angle_d13.8351943
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 (%)
1.808-1.87260.30443450.24846538688399
1.8726-1.94760.2413480.208766136961100
1.9476-2.03620.2233490.182866196968100
2.0362-2.14360.19973490.166666446993100
2.1436-2.27780.21773500.168366236973100
2.2778-2.45370.24433490.177566406989100
2.4537-2.70060.21413490.176966667015100
2.7006-3.09120.22513530.176666767029100
3.0912-3.89410.20043260.16276248657493
3.8941-40.64320.17923560.15596743709998
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)
13.3213-1.72241.34291.9811-0.16214.47820.16080.10960.0379-0.2182-0.05990.0539-0.29250.0756-0.11150.15410.0081-0.0030.0826-0.02720.1543158.90513.7168-3.223
25.02-2.05291.52233.9144-1.23982.02320.14020.2606-0.219-0.4718-0.02210.534-0.0292-0.4225-0.08830.26970.1072-0.1390.1977-0.11210.2881146.566412.4577-9.8014
34.11740.1111.09010.4246-0.20820.5617-0.0468-0.18470.54850.0011-0.0963-0.1461-0.022-0.02470.13150.15060.028-0.0250.1966-0.01980.2179187.71547.361514.0405
43.61010.13570.4542.156-0.25661.49660.0621-1.2568-0.33590.4637-0.0907-0.27940.1632-0.13690.01960.24990.0417-0.03540.48840.07130.1504179.5959-0.842722.6367
51.37730.40220.0610.9637-0.09071.193-0.0185-0.7834-0.52540.23070.02170.01630.137-0.03820.03230.1957-0.01490.01210.31580.05610.1896178.3059-8.243116.2337
62.3255-0.1171.2506-0.12160.10380.98270.0124-0.1646-0.11360.01240.0226-0.00610.066-0.1004-0.04550.14-0.00680.00510.13370.01940.1746193.7216-3.594716.1334
73.90330.14990.74842.96370.30973.6521-0.0135-0.41860.01150.1568-0.020.1240.0263-0.49580.01580.21070.01710.02260.26560.0130.1422221.6192-7.377737.6125
85.4384-4.14342.26225.4554-1.77472.4532-0.1517-0.54430.02470.15370.18040.1744-0.0381-0.3404-0.01960.1365-0.00810.0140.1809-0.00270.1359209.4878-4.487824.8669
93.5388-3.54151.93293.5399-1.7974.6459-0.0369-0.0209-1.08420.1950.4802-0.10180.60340.1963-0.43260.3891-0.0005-0.01060.216-0.00880.4373214.6825-18.493822.6287
106.87592.3159-4.75954.27992.64998.4613-0.0185-0.3292-0.19240.11-0.126-0.25150.40430.3060.14330.7680.10610.16890.62130.19351.1804209.9774-22.297426.4473
114.0566-1.05180.54741.6808-0.74290.5767-0.5297-0.8555-0.73690.62580.18210.01770.117-0.28370.23080.2661-0.07590.02740.41130.1220.2715207.0293-10.786427.7525
122.4283-0.7454-0.10680.8720.4320.76610.00540.10640.006-0.0981-0.03160.08540.0114-0.09210.03960.1486-0.00370.00520.14770.01890.1347220.0655-4.037411.1858
133.348-0.43940.93710.8952-0.25551.9046-0.13490.01160.19410.0660.0147-0.02-0.22210.06170.06810.1292-0.0001-0.00580.0735-0.00630.0869240.27183.923622.8399
145.2484.4468-4.47665.3538-4.29584.0157-0.0893-0.2964-0.3751-0.0462-0.0285-0.3350.32990.39080.09420.18050.0437-0.0320.17580.00560.1336248.5574-12.953530.5729
151.482-0.09570.39670.64430.0781.5026-0.03330.1211-0.0183-0.01130.0301-0.0250.03750.12570.00130.0989-0.01430.00960.0855-0.00880.103236.6217-2.280217.8464
161.3099-0.25770.04653.3804-0.1871.3276-0.0322-0.21060.05540.04950.08390.0955-0.05020.0138-0.04490.13250.0123-0.00330.1512-0.00790.0805237.7507-0.916632.4854
172.1228-1.11961.29961.8151-1.1371.3308-0.07860.14080.15980.0475-0.04960.03170.05850.03660.14790.16930.02380.00630.1796-0.00070.2265210.73523.918519.6165
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 375:377)A375 - 377
11X-RAY DIFFRACTION11(chain A and resid 384:402)A384 - 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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