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- PDB-5i8u: Crystal Structure of the RV1700 (MT ADPRASE) E142Q mutant -

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Basic information

Entry
Database: PDB / ID: 5i8u
TitleCrystal Structure of the RV1700 (MT ADPRASE) E142Q mutant
ComponentsADP-ribose pyrophosphatase
KeywordsHYDROLASE / NUDIX / nudix hydrolase / ADP-ribose hydrolase / ADPRase / ADPr hydrolase
Function / homology
Function and homology information


8-oxo-dGDP phosphatase / ADP-ribose diphosphatase / 8-oxo-GDP phosphatase activity / ADP-ribose diphosphatase activity / 8-oxo-dGDP phosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / DNA replication / DNA repair / metal ion binding / cytosol
Similarity search - Function
Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / Nudix hydrolase / ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsThirawatananond, P. / Kang, L.-W. / Amzel, L.M. / Gabelli, S.B.
CitationJournal: J. Bioenerg. Biomembr. / Year: 2016
Title: Kinetic and mutational studies of the adenosine diphosphate ribose hydrolase from Mycobacterium tuberculosis.
Authors: O'Handley, S.F. / Thirawatananond, P. / Kang, L.W. / Cunningham, J.E. / Leyva, J.A. / Amzel, L.M. / Gabelli, S.B.
History
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Sep 27, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: ADP-ribose pyrophosphatase
A: ADP-ribose pyrophosphatase
B: ADP-ribose pyrophosphatase
C: ADP-ribose pyrophosphatase
D: ADP-ribose pyrophosphatase
E: ADP-ribose pyrophosphatase
F: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,97115
Polymers160,4397
Non-polymers5328
Water10,935607
1
G: ADP-ribose pyrophosphatase
hetero molecules

G: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0324
Polymers45,8402
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5650 Å2
ΔGint-66 kcal/mol
Surface area16190 Å2
MethodPISA
2
A: ADP-ribose pyrophosphatase
B: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0885
Polymers45,8402
Non-polymers2483
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-50 kcal/mol
Surface area17140 Å2
MethodPISA
3
C: ADP-ribose pyrophosphatase
D: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0286
Polymers45,8402
Non-polymers1884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-73 kcal/mol
Surface area16700 Å2
MethodPISA
4
E: ADP-ribose pyrophosphatase
F: ADP-ribose pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)45,8402
Polymers45,8402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-34 kcal/mol
Surface area16170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.768, 124.844, 142.959
Angle α, β, γ (deg.)90.000, 98.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 7 molecules GABCDEF

#1: Protein
ADP-ribose pyrophosphatase / Nudix hydrolase


Mass: 22919.861 Da / Num. of mol.: 7 / Mutation: E142Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: TBPG_001531 / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)
References: UniProt: A0A045KHE5, UniProt: I6X235*PLUS, ADP-ribose diphosphatase

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Non-polymers , 5 types, 615 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 4.2 Å3/Da / Density % sol: 70.73 %
Crystal growMethod: vapor diffusion / Details: sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.502 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 1.99→141.42 Å / Num. obs: 159897 / % possible obs: 88.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.079 / Χ2: 0.729 / Net I/av σ(I): 10.734 / Net I/σ(I): 6.2 / Num. measured all: 510316
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.99-2.061.80.917101480.54556.2
2.06-2.142.20.903136710.53675.7
2.14-2.242.40.795143810.54479.6
2.24-2.362.70.722147140.67681.7
2.36-2.5130.603165900.6191.9
2.51-2.73.60.412179030.60299.1
2.7-2.973.70.216180820.60799.6
2.97-3.43.80.093180590.65399.8
3.4-4.293.80.051181300.93199.9
4.29-503.80.035182191.199.3

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1MK1

1mk1


Resolution: 2→141.42 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2577 / WRfactor Rwork: 0.2217 / FOM work R set: 0.7137 / SU B: 15.747 / SU ML: 0.165 / SU R Cruickshank DPI: 0.155 / SU Rfree: 0.1504 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 7975 5.1 %RANDOM
Rwork0.2217 ---
obs0.2235 149859 88.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 211.97 Å2 / Biso mean: 64.41 Å2 / Biso min: 12.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å2-1.6 Å2
2--1.12 Å20 Å2
3----2.15 Å2
Refinement stepCycle: final / Resolution: 2→141.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10713 0 30 607 11350
Biso mean--94.32 56.84 -
Num. residues----1378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01910969
X-RAY DIFFRACTIONr_angle_refined_deg2.0451.94814937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.03851366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85122.069522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.708151684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.37415135
X-RAY DIFFRACTIONr_chiral_restr0.1430.21677
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218511
X-RAY DIFFRACTIONr_mcbond_it3.0814.4055500
X-RAY DIFFRACTIONr_mcangle_it5.0256.5726854
X-RAY DIFFRACTIONr_scbond_it3.3294.6715469
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 402 -
Rwork0.38 6738 -
all-7140 -
obs--53.9 %
Refinement TLS params.

Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å / 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)
10.04880.17860.13190.68790.40680.82050.0891-0.0316-0.02460.2746-0.0962-0.12430.3823-0.04710.00710.1977-0.0442-0.00450.04740.02090.1511
20.66110.42170.85220.30520.61281.29920.55640.0392-0.4220.4155-0.0151-0.27260.84770.0202-0.54140.5912-0.0506-0.32970.1161-0.05640.3168
30.32040.23490.30010.37510.18991.04170.07810.1268-0.1721-0.00180.1108-0.03460.5493-0.0681-0.18890.3287-0.0957-0.07120.1813-0.14560.2241
40.16080.01570.18670.13470.36751.34060.12640.0658-0.09450.1766-0.1110.01230.607-0.157-0.01540.3051-0.0843-0.04290.1766-0.01520.1199
51.43130.16851.13460.23380.27751.50970.39210.5863-0.58320.19070.047-0.07710.74650.4404-0.43910.44830.1145-0.15460.2697-0.22960.2417
62.54321.13980.06020.86760.05130.3039-0.19460.2371-1.4522-0.37350.2737-0.73520.1855-0.1613-0.07910.3905-0.27650.15160.2061-0.15160.8543
70.85720.75310.16830.85710.07580.0877-0.03730.0627-0.3297-0.19890.122-0.25950.02770.0249-0.08470.1676-0.0928-0.00740.0759-0.02720.1495
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G5 - 206
2X-RAY DIFFRACTION2A5 - 207
3X-RAY DIFFRACTION3B6 - 207
4X-RAY DIFFRACTION4C5 - 207
5X-RAY DIFFRACTION5D5 - 207
6X-RAY DIFFRACTION6E6 - 206
7X-RAY DIFFRACTION7F6 - 206

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