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- PDB-1mk1: Structure of the MT-ADPRase in complex with ADPR, a Nudix enzyme -

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Basic information

Entry
Database: PDB / ID: 1mk1
TitleStructure of the MT-ADPRase in complex with ADPR, a Nudix enzyme
ComponentsADPR pyrophosphatase
KeywordsHYDROLASE / Nudix hydrolase / ADPR pyrophosphatase / ADPRase / Adenosine diphospho-ribose / Mycobacterium Tuberculosis / Rv1700
Function / homology
Function and homology information


nucleoside phosphate metabolic process / ribose phosphate metabolic process / manganese 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
ADENOSINE-5-DIPHOSPHORIBOSE / MutT/nudix family protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsKang, L.-W. / Gabelli, S.B. / Bianchet, M.A. / Cunningham, J.E. / O'Handley, S.F. / Amzel, L.M.
CitationJournal: Structure / Year: 2003
Title: Structure and mechanism of MT-ADPRase, a Nudix hydrolase from Mycobacterium tuberculosis
Authors: Kang, L.-W. / Gabelli, S.B. / Cunningham, J.E. / O'Handley, S.F. / Amzel, L.M.
History
DepositionAug 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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

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Assembly

Deposited unit
A: ADPR pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4802
Polymers22,9211
Non-polymers5591
Water1,820101
1
A: ADPR pyrophosphatase
hetero molecules

A: ADPR pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9604
Polymers45,8422
Non-polymers1,1192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area7170 Å2
ΔGint-48 kcal/mol
Surface area15890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.088, 64.088, 182.393
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein ADPR pyrophosphatase / ADPRase / MutT/nudix family protein / Hypothetical protein Rv1700


Mass: 22920.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1700 / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: O33199, ADP-ribose diphosphatase
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


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


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Sodium formate, Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
31 mMEDTA1drop
44.3 Msodium formate1reservoir
5100 mMTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 19, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 14597 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.054 / Net I/σ(I): 19.8
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 5.86 / Rsym value: 0.281 / % possible all: 94.8
Reflection
*PLUS
% possible obs: 92.4 % / Num. measured all: 97257 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 91.3 % / Mean I/σ(I) obs: 5.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 1484 -random
Rwork0.2086 ---
all-15802 --
obs-14597 92.4 %-
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 36 101 1600
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006569
X-RAY DIFFRACTIONc_angle_deg1.4395
X-RAY DIFFRACTIONc_mcbond_it1.25
X-RAY DIFFRACTIONc_mcangle_it2.16
Refinement
*PLUS
Rfactor Rfree: 0.259 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.44

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