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- PDB-7d56: Structure of the peptidylarginine deiminase type III (PAD3) in co... -

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Basic information

Entry
Database: PDB / ID: 7d56
TitleStructure of the peptidylarginine deiminase type III (PAD3) in complex with Cl-amidine
ComponentsProtein-arginine deiminase type-3
KeywordsHYDROLASE / Posttransrational modification / citrullination / calcium-dependent / calcium metabolism / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


protein-arginine deiminase / protein-arginine deiminase activity / Chromatin modifying enzymes / intracellular membrane-bounded organelle / calcium ion binding / nucleoplasm / identical protein binding / 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
Chem-BFB / Protein-arginine deiminase type-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.175 Å
AuthorsFunabashi, K. / Unno, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP2512704 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP23121504 Japan
Japan Society for the Promotion of Science (JSPS)JP19K06507 Japan
CitationJournal: Arch.Biochem.Biophys. / Year: 2021
Title: Structures of human peptidylarginine deiminase type III provide insights into substrate recognition and inhibitor design.
Authors: Funabashi, K. / Sawata, M. / Nagai, A. / Akimoto, M. / Mashimo, R. / Takahara, H. / Kizawa, K. / Thompson, P.R. / Ite, K. / Kitanishi, K. / Unno, M.
History
DepositionSep 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Protein-arginine deiminase type-3
B: Protein-arginine deiminase type-3
A: Protein-arginine deiminase type-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,62137
Polymers224,4873
Non-polymers2,13434
Water23413
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C: Protein-arginine deiminase type-3
hetero molecules

C: Protein-arginine deiminase type-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,14426
Polymers149,6582
Non-polymers1,48524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6840 Å2
ΔGint-144 kcal/mol
Surface area53160 Å2
MethodPISA
2
B: Protein-arginine deiminase type-3
A: Protein-arginine deiminase type-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,04924
Polymers149,6582
Non-polymers1,39122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-163 kcal/mol
Surface area52470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.577, 115.343, 127.844
Angle α, β, γ (deg.)90.000, 121.380, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 34 or (resid 35...
21(chain B and (resid 1 through 157 or (resid 158...
31(chain C and (resid 1 through 34 or (resid 35...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPROPRO(chain A and (resid 1 through 34 or (resid 35...AC1 - 341 - 34
12GLUGLUGLUGLU(chain A and (resid 1 through 34 or (resid 35...AC3535
13METMETPROPRO(chain A and (resid 1 through 34 or (resid 35...AC1 - 6641 - 664
14METMETPROPRO(chain A and (resid 1 through 34 or (resid 35...AC1 - 6641 - 664
15METMETPROPRO(chain A and (resid 1 through 34 or (resid 35...AC1 - 6641 - 664
21METMETASPASP(chain B and (resid 1 through 157 or (resid 158...BB1 - 1571 - 157
22ASPASPASPASP(chain B and (resid 1 through 157 or (resid 158...BB158158
23METMETPROPRO(chain B and (resid 1 through 157 or (resid 158...BB1 - 6641 - 664
24METMETPROPRO(chain B and (resid 1 through 157 or (resid 158...BB1 - 6641 - 664
25METMETPROPRO(chain B and (resid 1 through 157 or (resid 158...BB1 - 6641 - 664
26METMETPROPRO(chain B and (resid 1 through 157 or (resid 158...BB1 - 6641 - 664
31METMETPROPRO(chain C and (resid 1 through 34 or (resid 35...CA1 - 341 - 34
32GLUGLUGLUGLU(chain C and (resid 1 through 34 or (resid 35...CA3535
33METMETPROPRO(chain C and (resid 1 through 34 or (resid 35...CA1 - 6641 - 664
34METMETPROPRO(chain C and (resid 1 through 34 or (resid 35...CA1 - 6641 - 664
35METMETPROPRO(chain C and (resid 1 through 34 or (resid 35...CA1 - 6641 - 664
36METMETPROPRO(chain C and (resid 1 through 34 or (resid 35...CA1 - 6641 - 664

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Components

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Protein , 1 types, 3 molecules CBA

#1: Protein Protein-arginine deiminase type-3 / Peptidylarginine deiminase III / Protein-arginine deiminase type III


Mass: 74829.102 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI3, PAD3, PDI3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULW8, protein-arginine deiminase

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Non-polymers , 6 types, 47 molecules

#2: Chemical ChemComp-BFB / N-[(1S)-1-(AMINOCARBONYL)-4-(ETHANIMIDOYLAMINO)BUTYL]BENZAMIDE / (S)-N-ALPHA-BENZOYL-N5-(2-FLUORO-1-IMINOETHYL)-L-ORNITHINE AMIDE


Mass: 276.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: HEPES, pH 7.5, PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.17→49.363 Å / Num. obs: 41732 / % possible obs: 99.1 % / Redundancy: 3.523 % / Biso Wilson estimate: 71.192 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.069 / Χ2: 1.019 / Net I/σ(I): 16.66 / Num. measured all: 147011
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.17-3.373.5740.3923.2123493674865740.9240.46197.4
3.37-3.63.6210.2095.7522789631362940.9750.24599.7
3.6-3.883.5550.1219.4320948591258930.9890.14399.7
3.88-4.253.3650.07214.2518375548354600.9980.08699.6
4.25-4.753.3270.04621.6416306492449010.9980.05599.5
4.75-5.483.4010.03925.0814731435843320.9980.04799.4
5.48-6.693.7680.0427.6414023374037220.9980.04799.5
6.69-9.373.70.02936.6610668289828830.9990.03399.5
9.37-49.3633.3940.02248.695678171716730.9990.02697.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D4Y

7d4y


Resolution: 3.175→49.363 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2969 2087 5.01 %
Rwork0.2422 39584 -
obs0.245 41671 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 200.64 Å2 / Biso mean: 91.7923 Å2 / Biso min: 45.19 Å2
Refinement stepCycle: final / Resolution: 3.175→49.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14820 0 105 13 14938
Biso mean--89.99 53.43 -
Num. residues----1912
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8810X-RAY DIFFRACTION8.973TORSIONAL
12B8810X-RAY DIFFRACTION8.973TORSIONAL
13C8810X-RAY DIFFRACTION8.973TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.175-3.24860.37561300.3369244894
3.2486-3.32980.40891390.3092640100
3.3298-3.41980.32951380.2822618100
3.4198-3.52040.35641410.29462671100
3.5204-3.6340.35671380.28742634100
3.634-3.76390.3181410.27682660100
3.7639-3.91450.30881380.25642627100
3.9145-4.09260.34191390.26732636100
4.0926-4.30820.31571400.23512652100
4.3082-4.5780.28381380.21052630100
4.578-4.93110.25581400.21372667100
4.9311-5.42680.29151390.21372638100
5.4268-6.21080.29741400.23842664100
6.2108-7.81990.27871420.24912690100
7.8199-49.3630.24451440.2123270999
Refinement TLS params.Method: refined / Origin x: 43.6326 Å / Origin y: -30.4245 Å / Origin z: 54.8947 Å
111213212223313233
T0.5405 Å20.0279 Å20.0177 Å2-0.6831 Å20.0846 Å2--0.551 Å2
L0.1931 °20.1067 °20.04 °2-0.1329 °2-0.1002 °2--0.9508 °2
S0.0778 Å °0.0086 Å °0.016 Å °0.0176 Å °0.1079 Å °0.0765 Å °0.0054 Å °-0.3641 Å °-0.1846 Å °
Refinement TLS groupSelection details: all

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