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- PDB-3hfw: Crystal Structure of human ADP-ribosylhydrolase 1 (hARH1) -

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Basic information

Entry
Database: PDB / ID: 3hfw
TitleCrystal Structure of human ADP-ribosylhydrolase 1 (hARH1)
ComponentsProtein ADP-ribosylarginine hydrolase
KeywordsHYDROLASE / all alpha-helical / Magnesium
Function / homology
Function and homology information


[protein ADP-ribosylarginine] hydrolase / ADP-ribosylarginine hydrolase activity / protein de-ADP-ribosylation / potassium ion binding / protein modification process / magnesium ion binding / extracellular space
Similarity search - Function
ADP-ribosylarginine hydrolase / ADP-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / : / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / ADP-ribosylhydrolase ARH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsMueller-Dieckmann, C. / Weiss, M.S. / Mueller-Dieckmann, J. / Koch-Nolte, F.
CitationJournal: To be Published
Title: Crystal Structure of human ADP-ribosylhydrolase 1
Authors: Koch-Nolte, F. / Mueller-Dieckmann, J. / Weiss, M.S. / Mueller-Dieckmann, C.
History
DepositionMay 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 4, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein ADP-ribosylarginine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0805
Polymers39,5541
Non-polymers5264
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.280, 52.790, 140.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein ADP-ribosylarginine hydrolase / ADP-ribosylarginine hydrolase / ADP-ribose-L-arginine cleaving enzyme


Mass: 39553.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P54922, [protein ADP-ribosylarginine] hydrolase

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Non-polymers , 5 types, 134 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 150 mM Li-acetate, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.8505 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8505 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 26290 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 29.9 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 29.7
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 3 / Num. unique all: 0 / % possible all: 71.1

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Processing

SoftwareName: REFMAC / Version: 5.5.0070 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.92→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.007 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18527 1029 3.9 %RANDOM
Rwork0.15458 ---
obs0.15578 25262 99.39 %-
all-0 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.114 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å20 Å20 Å2
2---1.25 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.92→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 30 130 2943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212895
X-RAY DIFFRACTIONr_bond_other_d0.0010.021941
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9513929
X-RAY DIFFRACTIONr_angle_other_deg0.99734700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.475358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67923.561132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79615454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7991515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02623
X-RAY DIFFRACTIONr_mcbond_it0.8511.51764
X-RAY DIFFRACTIONr_mcbond_other0.2241.5738
X-RAY DIFFRACTIONr_mcangle_it1.5632.52790
X-RAY DIFFRACTIONr_scbond_it3.79851131
X-RAY DIFFRACTIONr_scangle_it5.802101138
LS refinement shellResolution: 1.92→1.971 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 61 -
Rwork0.241 1760 -
obs--94.01 %
Refinement TLS params.Method: refined / Origin x: 27.9549 Å / Origin y: 12.5936 Å / Origin z: 16.7918 Å
111213212223313233
T0.0078 Å20.0152 Å20.009 Å2-0.0612 Å20 Å2--0.0412 Å2
L1.1906 °20.5071 °2-0.4436 °2-2.1169 °2-0.2226 °2--1.8092 °2
S0.0282 Å °0.0245 Å °0.0522 Å °-0.0323 Å °-0.0011 Å °0.0016 Å °-0.0337 Å °0.0796 Å °-0.0271 Å °

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