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- PDB-4ijx: Crystal structure of human Ap4A hydrolase E58A mutant complexed w... -

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Basic information

Entry
Database: PDB / ID: 4ijx
TitleCrystal structure of human Ap4A hydrolase E58A mutant complexed with DPO
ComponentsBis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
KeywordsHYDROLASE / NUDIX FOLD
Function / homology
Function and homology information


bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity / AMP biosynthetic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / ATP biosynthetic process / nucleobase-containing compound metabolic process / Detoxification of Reactive Oxygen Species / cellular response to oxidative stress / mitochondrial matrix / apoptotic process / GTP binding
Similarity search - Function
Bis(5'-nucleosyl)-tetraphosphatase / : / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Bis(5'-nucleosyl)-tetraphosphatase / : / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHATE / PHOSPHATE ION / Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGe, H. / Chen, X.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Crystal structure of wild-type and mutant human Ap4A hydrolase.
Authors: Ge, H. / Chen, X. / Yang, W. / Niu, L. / Teng, M.
History
DepositionDec 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
B: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2097
Polymers35,7292
Non-polymers4805
Water2,180121
1
A: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1554
Polymers17,8641
Non-polymers2903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0543
Polymers17,8641
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
hetero molecules

B: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2097
Polymers35,7292
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455y-1,x,-z1
Buried area2430 Å2
ΔGint-21 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.369, 72.369, 133.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical] / Diadenosine 5' / 5'''-P1 / P4-tetraphosphate asymmetrical hydrolase / Ap4A hydrolase / Ap4Aase / ...Diadenosine 5' / 5'''-P1 / P4-tetraphosphate asymmetrical hydrolase / Ap4A hydrolase / Ap4Aase / Diadenosine tetraphosphatase / Nucleoside diphosphate-linked moiety X motif 2 / Nudix motif 2


Mass: 17864.350 Da / Num. of mol.: 2 / Mutation: E58A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT2, APAH1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P50583, bis(5'-nucleosyl)-tetraphosphatase (asymmetrical)

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Non-polymers , 5 types, 126 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.1M Tris, 2.0M Ammonium phosphate monobasic, 5mM magnesium chloride, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorDate: Jun 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 21348 / Num. obs: 20214
Reflection shellResolution: 2.103→2.157 Å / Num. unique all: 1277 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3u53

3u53


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.654 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23205 1098 5.2 %RANDOM
Rwork0.18862 ---
obs0.19079 20214 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-0 Å2
2--0.32 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 26 121 2481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192472
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.963357
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2265303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60924.32125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11715435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6441516
X-RAY DIFFRACTIONr_chiral_restr0.1230.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211881
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.103→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 82 -
Rwork0.206 1277 -
obs--98.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.46010.5286-0.3650.6212-0.40060.3229-0.12410.0731-0.1099-0.14850.0754-0.14430.0323-0.04750.04870.102-0.03410.05130.0264-0.02780.0592-8.063823.26014.4822
20.63540.42520.06930.99640.10440.40870.0601-0.12280.00220.1012-0.01160.0736-0.0898-0.1095-0.04850.04310.00850.02890.0819-00.0315-12.786334.420116.1955
30.14020.3366-0.19211.0972-0.20180.87720.0633-0.0252-0.01310.0115-0.07890.0012-0.1367-0.00390.01560.0653-0.0018-0.00720.0185-0.00880.0311-8.348136.22249.1461
41.15050.0809-0.61260.6816-0.28841.0815-0.0020.09680.02-0.08620.01160.01330.0701-0.1339-0.00960.0223-0.01890.01030.038-0.01610.0152-11.367629.34244.0932
51.13010.30470.90021.9032-0.35410.9261-0.127-0.1615-0.0597-0.04990.0532-0.2238-0.1339-0.14430.07380.0597-0.01030.00290.05470.00030.06859.18446.3498-5.2131
61.53950.28880.24761.65980.26460.12470.09530.13770.2228-0.2012-0.11210.0173-0.0588-0.00170.01680.08620.01890.0190.0370.03060.03890.190251.9631-11.7856
71.36070.1027-0.24310.80420.07730.5347-0.09160.1286-0.0111-0.05840.0425-0.0134-0.0619-0.05470.04910.0472-0.0155-0.00350.0215-0.00440.00673.19349.6753-9.8684
81.76180.32430.44951.3779-0.7940.70160.0128-0.1479-0.07170.1898-0.00390.0333-0.1421-0.0272-0.00890.064-0.02590.00470.03380.00050.03224.336346.48322.9432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 26
2X-RAY DIFFRACTION2A27 - 69
3X-RAY DIFFRACTION3A70 - 102
4X-RAY DIFFRACTION4A103 - 150
5X-RAY DIFFRACTION5B3 - 23
6X-RAY DIFFRACTION6B24 - 60
7X-RAY DIFFRACTION7B61 - 117
8X-RAY DIFFRACTION8B118 - 148

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