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- PDB-4ick: Crystal structure of human AP4A hydrolase E58A mutant -

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Basic information

Entry
Database: PDB / ID: 4ick
TitleCrystal structure of human AP4A hydrolase E58A mutant
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 / GTP binding / apoptotic process
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
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 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)35,9405
Polymers35,7292
Non-polymers2113
Water3,333185
1
A: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9562
Polymers17,8641
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9843
Polymers17,8641
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.190, 72.190, 133.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#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)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.1M Tris (pH 8.4), 2.0M Ammonium phosphate monobasic, 5mM magnesium chloride, temperature 285K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.00584 Å
DetectorDate: May 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00584 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 21385 / Num. obs: 20197 / % possible obs: 100 % / Observed criterion σ(I): 13.7
Reflection shellResolution: 2.1→2.154 Å / % possible all: 99.77

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U53

3u53


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.649 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23464 1094 5.1 %RANDOM
Rwork0.18645 ---
obs0.1889 20197 99.77 %-
all-21385 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.849 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å20 Å2
2--0.13 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 12 185 2535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192422
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9583279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8245295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02324.38121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75315431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3851515
X-RAY DIFFRACTIONr_chiral_restr0.1070.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211838
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 69 -
Rwork0.212 1291 -
obs--99.78 %
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)
11.1879-0.0318-1.18663.2030.54791.307-0.27370.1392-0.2076-0.29140.1332-0.26540.1231-0.11380.14050.2371-0.05840.07010.0903-0.03870.1331-8.225423.21034.394
21.21341.1250.48481.34810.40291.10510.0593-0.16540.0470.1396-0.0780.0979-0.2078-0.23060.01870.12950.01040.00550.1291-0.03410.0861-12.819434.155516.2291
30.23420.408-0.37821.0502-0.28381.31550.099-0-0.00930.0638-0.0774-0.0074-0.1702-0.0353-0.02160.1120.02150.01370.1058-0.00970.0965-8.507636.03329.0659
41.72240.234-0.94151.344-0.24291.5328-0.00630.15480.0299-0.1306-0.01050.02210.0846-0.17030.01680.0599-0.0205-0.00050.0896-0.0280.0728-11.518629.12684.1992
56.91330.52871.58883.0550.44640.4538-0.054-0.4908-0.0467-0.06870.0108-0.2455-0.0511-0.17490.04320.11310.01620.0210.1506-0.04820.13038.964146.3375-5.5534
62.35590.41690.17293.21460.29780.0480.15640.21520.2201-0.3919-0.160.0209-0.0573-0.01890.00360.18380.05420.0130.11910.03090.0550.120351.5406-11.9176
72.02380.0011-0.52071.2062-0.12130.8021-0.08920.2084-0.0408-0.09260.0518-0.0316-0.0978-0.08970.03740.1172-0.01470.0140.0645-0.00690.05663.018949.4332-9.91
82.51710.39450.18581.6346-0.90450.71740.0646-0.1989-0.15060.2265-0.04850.1114-0.20830.0738-0.01610.1564-0.04670.00320.1024-0.00440.10284.120746.3282.9117
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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