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- PDB-9b98: Crystal structure of the human PAD2 protein bound to small molecule -

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Basic information

Entry
Database: PDB / ID: 9b98
TitleCrystal structure of the human PAD2 protein bound to small molecule
ComponentsProtein-arginine deiminase type-2
KeywordsHYDROLASE / Complex
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 / 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 / Cupredoxin
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: 2.003 Å
AuthorsByrnes, L.J. / Vajdos, F.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Discovery, Characterization, and Structure of a Cell Active PAD2 Inhibitor Acting through a Novel Allosteric Mechanism.
Authors: Byrnes, L.J. / Choi, W.Y. / Balbo, P. / Banker, M.E. / Chang, J. / Chen, S. / Cheng, X. / Cong, Y. / Culp, J. / Di, H. / Griffor, M. / Hall, J. / Meng, X. / Morgan, B. / Mousseau, J.J. / ...Authors: Byrnes, L.J. / Choi, W.Y. / Balbo, P. / Banker, M.E. / Chang, J. / Chen, S. / Cheng, X. / Cong, Y. / Culp, J. / Di, H. / Griffor, M. / Hall, J. / Meng, X. / Morgan, B. / Mousseau, J.J. / Nicki, J. / O'Connell, T. / Ramsey, S. / Shaginian, A. / Shanker, S. / Trujillo, J. / Wan, J. / Vincent, F. / Wright, S.W. / Vajdos, F.
History
DepositionApr 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)79,7939
Polymers78,6731
Non-polymers1,1208
Water2,630146
1
A: Protein-arginine deiminase type-2
hetero molecules

A: Protein-arginine deiminase type-2
hetero molecules


  • defined by author&software
  • 160 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)159,58718
Polymers157,3462
Non-polymers2,24116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area6930 Å2
ΔGint-128 kcal/mol
Surface area50170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.710, 52.780, 76.590
Angle α, β, γ (deg.)90.000, 105.709, 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: 78673.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI2, KIAA0994, PAD2, PDI2 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sF9 / References: UniProt: Q9Y2J8, protein-arginine deiminase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-A1AJC / (5P)-N,N-diethyl-2-fluoro-5-(2-[({1-[2-(methylamino)-2-oxoethyl]cyclohexyl}methyl)amino]-6-{methyl[1-(2-methyl-1-phenyl-1H-1,3-benzimidazole-5-carbonyl)piperidin-4-yl]amino}pyrimidin-4-yl)benzamide


Mass: 801.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H56FN9O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Magnesium acetate, 50mM MES pH5.5, 9-16% 2-methyl 2, 4-pentane diol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.003→97.088 Å / Num. obs: 26935 / % possible obs: 92.2 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.025 / Rrim(I) all: 0.045 / Net I/σ(I): 16.3
Reflection shellResolution: 2.003→2.276 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1347 / CC1/2: 0.617 / Rpim(I) all: 0.483 / Rrim(I) all: 0.903 / % possible all: 75.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.003→97.088 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.651 / SU ML: 0.173 / Cross valid method: FREE R-VALUE / ESU R: 0.455 / ESU R Free: 0.291
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2575 1358 5.042 %
Rwork0.1857 25577 -
all0.189 --
obs-26935 51.213 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.135 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0.205 Å2
2--0.259 Å20 Å2
3----0.055 Å2
Refinement stepCycle: LAST / Resolution: 2.003→97.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4805 0 72 146 5023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125028
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164635
X-RAY DIFFRACTIONr_angle_refined_deg1.511.6366787
X-RAY DIFFRACTIONr_angle_other_deg0.5161.57110811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2095599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.0171030
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48710854
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.06410221
X-RAY DIFFRACTIONr_chiral_restr0.0690.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025774
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02978
X-RAY DIFFRACTIONr_nbd_refined0.2240.21024
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.24801
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22355
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22747
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1670.223
X-RAY DIFFRACTIONr_nbd_other0.1710.2129
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.211
X-RAY DIFFRACTIONr_mcbond_it5.486.0192419
X-RAY DIFFRACTIONr_mcbond_other5.4716.022413
X-RAY DIFFRACTIONr_mcangle_it8.18.9913000
X-RAY DIFFRACTIONr_mcangle_other8.0998.9923001
X-RAY DIFFRACTIONr_scbond_it5.4266.3922609
X-RAY DIFFRACTIONr_scbond_other5.4256.3922610
X-RAY DIFFRACTIONr_scangle_it8.2629.4253786
X-RAY DIFFRACTIONr_scangle_other8.269.4243787
X-RAY DIFFRACTIONr_lrange_it12.55276.4785510
X-RAY DIFFRACTIONr_lrange_other12.55176.4785511
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.003-2.0550.92420.396410.41838190.780.8981.12590.367
2.055-2.1120.34120.341530.3438230.8890.9184.3160.329
2.112-2.1730.377140.3073400.30936440.860.9269.71460.294
2.173-2.240.319240.2984490.29935250.920.93413.41840.282
2.24-2.3130.378250.2686570.27234660.9190.9519.67690.241
2.313-2.3940.31510.2878400.28833380.9480.94626.69260.247
2.394-2.4850.361600.27911930.28332310.9190.94738.78060.246
2.485-2.5860.332820.26714000.27131010.930.95247.7910.22
2.586-2.7010.348940.25816300.26229370.9190.95658.69940.213
2.701-2.8330.2911080.2618650.26228790.9460.95468.53070.208
2.833-2.9860.3281280.23920230.24427110.9280.96179.34340.201
2.986-3.1670.3181280.23821920.24225660.9330.96490.41310.2
3.167-3.3850.2951030.22623040.22924270.9360.96899.17590.193
3.385-3.6560.2511040.19321340.19622440.9620.97799.73260.175
3.656-4.0040.2281180.16519750.16821080.9660.98499.28840.16
4.004-4.4760.232830.14617790.14918890.9650.98798.57070.148
4.476-5.1660.194790.1315940.13316840.9810.9999.34680.142
5.166-6.3230.232650.1613340.16414110.9640.98499.14950.178
6.323-8.9230.232460.15610650.1611250.9660.98498.75560.184
8.923-97.0880.229320.1716090.1736540.9560.97498.01220.25

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