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- PDB-5hp5: Srtucture of human peptidylarginine deiminase type I (PAD1) -

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Basic information

Entry
Database: PDB / ID: 5hp5
TitleSrtucture of human peptidylarginine deiminase type I (PAD1)
ComponentsProtein-arginine deiminase type-1
KeywordsHYDROLASE / peptidylarginine deiminase / PAD1 / isozyme / monomer
Function / homology
Function and homology information


: / : / protein-arginine deiminase / protein-arginine deiminase activity / Chromatin modifying enzymes / chromatin organization / calcium ion binding / nucleoplasm / 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-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.198 Å
AuthorsUnno, M. / Nagai, A. / Saijo, S. / Shimizu, N. / Kinjo, S. / Mashimo, R. / Kizawa, K. / Takahara, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
MEXT23121504 Japan
MEXT25121704 Japan
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Monomeric Form of Peptidylarginine Deiminase Type I Revealed by X-ray Crystallography and Small-Angle X-ray Scattering
Authors: Saijo, S. / Nagai, A. / Kinjo, S. / Mashimo, R. / Akimoto, M. / Kizawa, K. / Yabe-Wada, T. / Shimizu, N. / Takahara, H. / Unno, M.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-arginine deiminase type-1
B: Protein-arginine deiminase type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,90110
Polymers154,5802
Non-polymers3218
Water30617
1
A: Protein-arginine deiminase type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4505
Polymers77,2901
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area29650 Å2
MethodPISA
2
B: Protein-arginine deiminase type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4505
Polymers77,2901
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area29620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.815, 90.815, 373.049
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein-arginine deiminase type-1 / Peptidylarginine deiminase I / Protein-arginine deiminase type I


Mass: 77290.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI1, PAD1, PDI1 / Production host: unidentified plasmid (others) / References: UniProt: Q9ULC6, protein-arginine deiminase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 50 mM citric acid, 0.2 M CaCl2, 15%(w/v) PEG3350, 14%(v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 28698 / % possible obs: 99.8 % / Redundancy: 11.6 % / Net I/σ(I): 20.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WDA

1wda


Resolution: 3.198→29.726 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 31.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2782 1441 5.05 %
Rwork0.213 --
obs0.2163 28555 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.198→29.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10556 0 8 17 10581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610824
X-RAY DIFFRACTIONf_angle_d1.36314684
X-RAY DIFFRACTIONf_dihedral_angle_d16.6444030
X-RAY DIFFRACTIONf_chiral_restr0.0481586
X-RAY DIFFRACTIONf_plane_restr0.0061926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1981-3.31220.35641470.27812692X-RAY DIFFRACTION99
3.3122-3.44470.29461450.26652715X-RAY DIFFRACTION100
3.4447-3.60120.31161300.2452728X-RAY DIFFRACTION100
3.6012-3.79070.31531300.24082746X-RAY DIFFRACTION100
3.7907-4.02770.29841440.23472684X-RAY DIFFRACTION100
4.0277-4.33780.28921510.21032712X-RAY DIFFRACTION100
4.3378-4.77270.24721310.18592746X-RAY DIFFRACTION100
4.7727-5.45960.27971530.19192675X-RAY DIFFRACTION100
5.4596-6.86450.24611540.22092713X-RAY DIFFRACTION100
6.8645-29.72750.26261560.18592703X-RAY DIFFRACTION99

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