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- PDB-3apm: Crystal structure of the human SNP PAD4 protein -

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Basic information

Entry
Database: PDB / ID: 3apm
TitleCrystal structure of the human SNP PAD4 protein
ComponentsProtein-arginine deiminase type-4
KeywordsHYDROLASE / alpha/beta-propeller / immunoglobulin-like / arginine citrullination / protein-arginine deiminase / post-translational modification / Calcium binding / histone binding / benzoyl-L-arginine amide binding / nucleus
Function / homology
Function and homology information


histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification ...histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification / protein modification process / nucleosome assembly / chromatin organization / chromatin remodeling / innate immune response / calcium ion binding / protein-containing complex / nucleoplasm / identical protein binding / 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-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHorikoshi, N. / Tachiwana, H. / Saito, K. / Osakabe, A. / Sato, M. / Yamada, M. / Akashi, S. / Nishimura, Y. / Kagawa, W. / Kurumizaka, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural and biochemical analyses of the human PAD4 variant encoded by a functional haplotype gene
Authors: Horikoshi, N. / Tachiwana, H. / Saito, K. / Osakabe, A. / Sato, M. / Yamada, M. / Akashi, S. / Nishimura, Y. / Kagawa, W. / Kurumizaka, H.
History
DepositionOct 19, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 1, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-arginine deiminase type-4


Theoretical massNumber of molelcules
Total (without water)74,4571
Polymers74,4571
Non-polymers00
Water0
1
A: Protein-arginine deiminase type-4

A: Protein-arginine deiminase type-4


Theoretical massNumber of molelcules
Total (without water)148,9152
Polymers148,9152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4900 Å2
ΔGint-13 kcal/mol
Surface area49050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.556, 61.239, 113.474
Angle α, β, γ (deg.)90.00, 123.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein-arginine deiminase type-4 / PAD4 / HL-60 PAD / Peptidylarginine deiminase IV / Protein-arginine deiminase type IV


Mass: 74457.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI4, PADI5, PDI5 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UM07, protein-arginine deiminase

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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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: imidazole, lithium sulfate, PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 14, 2010
RadiationMonochromator: Rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 29118 / Num. obs: 28960 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 64.5 Å2 / Rsym value: 0.065 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.5-2.593.8327630.641199.5
2.59-2.693.63.629110.526196.5
2.69-2.823.84.528710.4091100
2.82-2.963.86.928850.2721100
2.96-3.153.810.429160.1731100
3.15-3.393.816.529090.1031100
3.39-3.733.82828790.061100
3.73-4.273.838.129180.051100
4.27-5.383.745.129450.047199.9
5.38-503.749.229630.028198.3

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WD8

1wd8


Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1469 5.1 %RANDOM
Rwork0.26 ---
all0.286 28999 --
obs0.261 28927 --
Solvent computationBsol: 44.4812 Å2
Displacement parametersBiso mean: 66.6636 Å2
Baniso -1Baniso -2Baniso -3
1--10.823 Å20 Å2-5.015 Å2
2--25.585 Å20 Å2
3----14.762 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 0 0 4383
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.473
X-RAY DIFFRACTIONc_mcbond_it1.4831.5
X-RAY DIFFRACTIONc_scbond_it1.7972
X-RAY DIFFRACTIONc_mcangle_it2.6242
X-RAY DIFFRACTIONc_scangle_it2.7882.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
2.5-2.590.4621430.445X-RAY DIFFRACTION268610
2.59-2.690.4491390.387X-RAY DIFFRACTION275410
2.69-2.820.4131370.363X-RAY DIFFRACTION273510
2.82-2.960.3931350.341X-RAY DIFFRACTION274010
2.96-3.150.4061550.32X-RAY DIFFRACTION274410
3.15-3.390.2931530.288X-RAY DIFFRACTION273610
3.39-3.730.2681420.268X-RAY DIFFRACTION273410
3.73-4.270.281370.224X-RAY DIFFRACTION276610
4.27-5.380.2281670.201X-RAY DIFFRACTION276410
5.38-300.2371610.226X-RAY DIFFRACTION279910
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5cis_peptide.param

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