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- PDB-7d5r: Structure of the Ca2+-bound C646A mutant of peptidylarginine deim... -

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Basic information

Entry
Database: PDB / ID: 7d5r
TitleStructure of the Ca2+-bound C646A mutant of peptidylarginine deiminase type III (PAD3)
ComponentsProtein-arginine deiminase type-3
KeywordsHYDROLASE / deimination / citrullination / peptidylarginine deiminase / post-translational modification / enzyme / isozyme / mutant / 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
Protein-arginine deiminase type-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.148 Å
AuthorsMashimo, R. / Akimoto, M. / Unno, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19K06507. Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP25121704 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP23121504 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 28, 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
A: Protein-arginine deiminase type-3
B: Protein-arginine deiminase type-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,32118
Polymers149,5942
Non-polymers72716
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-152 kcal/mol
Surface area52050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.536, 114.536, 326.766
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 577 or (resid 578...
21(chain B and (resid 3 through 55 or (resid 56...

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
11LEULEUARGARG(chain A and (resid 3 through 577 or (resid 578...AA3 - 5773 - 577
12LYSLYSLYSLYS(chain A and (resid 3 through 577 or (resid 578...AA578578
13LEULEUPROPRO(chain A and (resid 3 through 577 or (resid 578...AA3 - 6643 - 664
14LEULEUPROPRO(chain A and (resid 3 through 577 or (resid 578...AA3 - 6643 - 664
15LEULEUPROPRO(chain A and (resid 3 through 577 or (resid 578...AA3 - 6643 - 664
16LEULEUPROPRO(chain A and (resid 3 through 577 or (resid 578...AA3 - 6643 - 664
21LEULEUASNASN(chain B and (resid 3 through 55 or (resid 56...BB3 - 553 - 55
22METMETMETMET(chain B and (resid 3 through 55 or (resid 56...BB5656
23LEULEUPROPRO(chain B and (resid 3 through 55 or (resid 56...BB3 - 6643 - 664
24LEULEUPROPRO(chain B and (resid 3 through 55 or (resid 56...BB3 - 6643 - 664
25LEULEUPROPRO(chain B and (resid 3 through 55 or (resid 56...BB3 - 6643 - 664
26LEULEUPROPRO(chain B and (resid 3 through 55 or (resid 56...BB3 - 6643 - 664

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Components

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


Mass: 74797.039 Da / Num. of mol.: 2 / Mutation: C646A
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
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: Tris-HCl, 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-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.148→50 Å / Num. obs: 27561 / % possible obs: 99.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.039 / Rrim(I) all: 0.087 / Χ2: 1.006 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.15-3.24.90.46313890.940.2350.520.6799.1
3.2-3.264.90.35613820.9710.1810.3990.67299.1
3.26-3.334.90.31713480.9730.1610.3560.66999.3
3.33-3.394.90.25313820.980.1290.2840.70499.3
3.39-3.474.90.20813870.9910.1060.2340.75299.4
3.47-3.554.90.2113820.9820.1060.2350.75599.3
3.55-3.644.90.16413580.9920.0830.1840.80999.3
3.64-3.734.90.1413950.9920.0710.1580.86699.5
3.73-3.844.90.11913600.9940.0610.1340.88199.4
3.84-3.974.90.10713960.9950.0540.120.93199.6
3.97-4.114.90.09313780.9960.0470.1050.9499.5
4.11-4.274.90.07813690.9970.040.0881.04699.6
4.27-4.474.90.06713670.9960.0340.0751.10699.6
4.47-4.74.90.06313900.9970.0320.071.2399.6
4.7-54.80.0613760.9970.030.0671.25699.7
5-5.384.80.05913930.9980.030.0671.30799.6
5.38-5.934.80.06113630.9950.0310.0691.80299.8
5.93-6.784.80.05313920.9970.0270.061.20399.9
6.78-8.544.60.04213920.9980.0220.0481.21599.7
8.54-504.80.03513620.9980.0180.0391.3698.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D4Y

7d4y


Resolution: 3.148→34.074 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 33.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2813 1289 4.69 %
Rwork0.2325 26170 -
obs0.2348 27459 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.11 Å2 / Biso mean: 84.9758 Å2 / Biso min: 36.75 Å2
Refinement stepCycle: final / Resolution: 3.148→34.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9847 0 26 0 9873
Biso mean--84.79 --
Num. residues----1253
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5716X-RAY DIFFRACTION12.238TORSIONAL
12B5716X-RAY DIFFRACTION12.238TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1482-3.27410.44571270.3131293498
3.2741-3.4230.31971520.2662286299
3.423-3.60330.32631450.2697288699
3.6033-3.82870.32331300.2427293799
3.8287-4.12390.32951440.2442291099
4.1239-4.5380.23571430.20572903100
4.538-5.19270.27561130.2035295299
5.1927-6.53470.23751540.23232905100
6.5347-34.0740.25881810.2203288199
Refinement TLS params.Method: refined / Origin x: 244.0153 Å / Origin y: 25.3267 Å / Origin z: -0.2993 Å
111213212223313233
T0.4978 Å2-0.0849 Å20.0611 Å2-0.3926 Å2-0.0244 Å2--0.5114 Å2
L0.1909 °2-0.0983 °20.4151 °2-0.0942 °2-0.2355 °2--1.9918 °2
S0.0688 Å °-0.0017 Å °0.025 Å °-0.0043 Å °0.0618 Å °-0.0028 Å °-0.2406 Å °0.1387 Å °0 Å °
Refinement TLS groupSelection details: all

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