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- PDB-6iux: Crystal structure of a hydrolase protein -

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Basic information

Entry
Database: PDB / ID: 6iux
TitleCrystal structure of a hydrolase protein
Components[Protein ADP-ribosylarginine] hydrolase
KeywordsHYDROLASE / ADPR / protein
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
Chem-AR6 / ADP-ribosylhydrolase ARH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.195 Å
AuthorsLiu, X.H. / Yu, X.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81672794 China
CitationJournal: To Be Published
Title: Crystal structure of protein
Authors: Liu, X.H. / Yu, X.C.
History
DepositionDec 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Assembly

Deposited unit
A: [Protein ADP-ribosylarginine] hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5563
Polymers41,9721
Non-polymers5842
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13300 Å2
Unit cell
Length a, b, c (Å)45.680, 52.919, 141.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 41972.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRH, ARH1 / Production host: Escherichia coli (E. coli)
References: UniProt: P54922, [protein ADP-ribosylarginine] hydrolase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium chloride pH 6.3, 20% PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.195→36 Å / Num. obs: 160794 / % possible obs: 77.6 % / Redundancy: 11.5 % / Net I/σ(I): 24.2
Reflection shellResolution: 1.2→1.26 Å

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Processing

Software
NameClassification
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.195→26.007 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1828 3790 2.36 %
Rwork0.1591 --
obs0.1597 160794 76.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.195→26.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 37 423 3248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062953
X-RAY DIFFRACTIONf_angle_d0.9594015
X-RAY DIFFRACTIONf_dihedral_angle_d8.8971664
X-RAY DIFFRACTIONf_chiral_restr0.074409
X-RAY DIFFRACTIONf_plane_restr0.005518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1954-1.21050.3625210.4661914X-RAY DIFFRACTION12
1.2105-1.22650.379360.36511473X-RAY DIFFRACTION19
1.2265-1.24330.3965440.35541920X-RAY DIFFRACTION26
1.2433-1.2610.2798560.30882386X-RAY DIFFRACTION31
1.261-1.27980.306680.28012845X-RAY DIFFRACTION38
1.2798-1.29980.1996800.21423370X-RAY DIFFRACTION44
1.2998-1.32120.1936960.19743906X-RAY DIFFRACTION52
1.3212-1.34390.2081050.19584424X-RAY DIFFRACTION58
1.3439-1.36840.20871210.19064949X-RAY DIFFRACTION66
1.3684-1.39470.26661300.19535376X-RAY DIFFRACTION71
1.3947-1.42320.17681520.18676375X-RAY DIFFRACTION84
1.4232-1.45410.22821700.18277073X-RAY DIFFRACTION94
1.4541-1.48790.21681780.16647341X-RAY DIFFRACTION97
1.4879-1.52510.17631830.16577417X-RAY DIFFRACTION98
1.5251-1.56640.16941810.16357440X-RAY DIFFRACTION99
1.5664-1.61240.18781840.16197493X-RAY DIFFRACTION99
1.6124-1.66450.21771800.16067490X-RAY DIFFRACTION99
1.6645-1.7240.20081830.16547478X-RAY DIFFRACTION99
1.724-1.7930.19481860.1617488X-RAY DIFFRACTION98
1.793-1.87450.16431810.1597508X-RAY DIFFRACTION99
1.8745-1.97330.18011840.15467508X-RAY DIFFRACTION100
1.9733-2.09690.18231820.15357573X-RAY DIFFRACTION100
2.0969-2.25870.15571780.15177551X-RAY DIFFRACTION100
2.2587-2.48590.17731780.14987420X-RAY DIFFRACTION98
2.4859-2.84520.16271830.15257532X-RAY DIFFRACTION99
2.8452-3.58320.1691770.14477570X-RAY DIFFRACTION100
3.5832-26.01320.18241730.14897184X-RAY DIFFRACTION95

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