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- PDB-7d8n: Structure of the inactive form of wild-type peptidylarginine deim... -

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Basic information

Entry
Database: PDB / ID: 7d8n
TitleStructure of the inactive form of wild-type peptidylarginine deiminase type III (PAD3) crystallized under the condition with high concentrations of Ca2+
ComponentsProtein-arginine deiminase type-3
KeywordsHYDROLASE / citrullination / inactive / isozyme / post-translational modification / calcium ion
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: 2.753 Å
AuthorsFunabashi, K. / Sawata, M. / Unno, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP25121704 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
DepositionOct 8, 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)150,77521
Polymers149,6582
Non-polymers1,11619
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-138 kcal/mol
Surface area51010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.874, 108.110, 93.560
Angle α, β, γ (deg.)90.000, 118.510, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 69 or (resid 70...
21(chain B and ((resid 2 through 3 and (name N...

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
11SERSERARGARG(chain A and (resid 2 through 69 or (resid 70...AA2 - 692 - 69
12PHEPHEPHEPHE(chain A and (resid 2 through 69 or (resid 70...AA7070
13SERSERPROPRO(chain A and (resid 2 through 69 or (resid 70...AA2 - 6642 - 664
14SERSERPROPRO(chain A and (resid 2 through 69 or (resid 70...AA2 - 6642 - 664
15SERSERPROPRO(chain A and (resid 2 through 69 or (resid 70...AA2 - 6642 - 664
21SERSERLEULEU(chain B and ((resid 2 through 3 and (name N...BB2 - 32 - 3
22SERSERPROPRO(chain B and ((resid 2 through 3 and (name N...BB2 - 6642 - 664
23SERSERPROPRO(chain B and ((resid 2 through 3 and (name N...BB2 - 6642 - 664
24SERSERPROPRO(chain B and ((resid 2 through 3 and (name N...BB2 - 6642 - 664
25SERSERPROPRO(chain B and ((resid 2 through 3 and (name N...BB2 - 6642 - 664

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Components

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


Mass: 74829.102 Da / Num. of mol.: 2
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.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: CaCl2, Tris-HCl, PEG 4000

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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 PILATUS 2M-F / Detector: PIXEL / Date: May 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 40408 / % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.042 / Rrim(I) all: 0.078 / Χ2: 1.019 / Net I/σ(I): 9.2 / Num. measured all: 139121
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.83.60.41419760.8710.2550.4870.48399.9
2.8-2.853.60.34620150.9030.2140.4080.465100
2.85-2.93.60.30420250.9190.1870.3570.502100
2.9-2.963.60.25920020.9340.1610.3050.504100
2.96-3.033.60.23220250.9370.1450.2740.545100
3.03-3.13.60.19120100.960.1190.2260.612100
3.1-3.173.50.17120200.9680.1070.2020.684100
3.17-3.263.50.13920280.9740.0870.1640.774100
3.26-3.363.50.12320030.9790.0780.1460.877100
3.36-3.463.40.10620290.9820.0680.1261.064100
3.46-3.593.40.09320320.9850.060.1111.13100
3.59-3.733.30.08220100.9880.0530.0981.405100
3.73-3.93.20.07119850.9910.0460.0851.43299.9
3.9-4.112.90.06220150.9910.0440.0761.6399.6
4.11-4.362.90.05520300.9920.0380.0671.68299.8
4.36-4.73.30.04720260.9950.030.0561.59699.8
4.7-5.173.70.04320220.9960.0260.0511.39199.5
5.17-5.923.70.04120300.9970.0250.0481.1999.9
5.92-7.463.70.03920480.9970.0240.0461.231100
7.46-503.40.03820770.9960.0240.0451.64599.6

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Processing

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

7d4y


Resolution: 2.753→46.717 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 2078 5.14 %
Rwork0.2049 38319 -
obs0.2073 40397 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.78 Å2 / Biso mean: 62.1187 Å2 / Biso min: 26.26 Å2
Refinement stepCycle: final / Resolution: 2.753→46.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9690 0 54 125 9869
Biso mean--86.92 51.71 -
Num. residues----1253
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5649X-RAY DIFFRACTION10.881TORSIONAL
12B5649X-RAY DIFFRACTION10.881TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.753-2.81690.35831270.2698234492
2.8169-2.88730.30631420.25552549100
2.8873-2.96530.34971330.25632561100
2.9653-3.05260.33051340.25852547100
3.0526-3.15110.29291230.24732590100
3.1511-3.26370.28191300.23072594100
3.2637-3.39430.27951260.23642572100
3.3943-3.54880.31450.22532524100
3.5488-3.73580.28151190.21482625100
3.7358-3.96970.29311500.19722534100
3.9697-4.2760.23841460.17832558100
4.276-4.7060.19231670.15872550100
4.706-5.38610.1871540.16572541100
5.3861-6.78260.23691420.19962594100
6.7826-46.7170.24041400.21372636100
Refinement TLS params.Method: refined / Origin x: -11.7544 Å / Origin y: 9.4989 Å / Origin z: 21.6078 Å
111213212223313233
T0.3139 Å2-0.0133 Å20.0411 Å2-0.3123 Å2-0.0052 Å2--0.2688 Å2
L1.0078 °20.2722 °20.4457 °2-0.3009 °20.2114 °2--0.5273 °2
S0.0496 Å °-0.0477 Å °0.0181 Å °0.0096 Å °-0.0433 Å °-0.001 Å °0.0145 Å °-0.0201 Å °-0.0028 Å °
Refinement TLS groupSelection details: all

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