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- PDB-1mqe: Structure of the MT-ADPRase in complex with gadolidium and ADP-ri... -

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Basic information

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


guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / UDP-sugar diphosphatase activity / ADP-sugar diphosphatase activity / 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 / GADOLINIUM ION / 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
DepositionSep 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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 / _struct_conn.ptnr2_label_seq_id / _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)23,6373
Polymers22,9211
Non-polymers7172
Water1,54986
1
A: ADPR pyrophosphatase
hetero molecules

A: ADPR pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2756
Polymers45,8422
Non-polymers1,4334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area7720 Å2
ΔGint-68 kcal/mol
Surface area15860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.052, 64.052, 182.212
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe second part of the biological assembly is generated by the two fold axis

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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) / 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: Chemical ChemComp-GD3 / GADOLINIUM ION


Mass: 157.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Gd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium formate, Tris HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
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: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 20, 2001 / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 15835 / Num. obs: 15604 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.075 / Net I/σ(I): 21.3
Reflection shellResolution: 2→2.07 Å / Rsym value: 0.336 / % possible all: 97.5
Reflection
*PLUS
Num. measured all: 127268 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 97.5 % / Mean I/σ(I) obs: 5.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 1560 random
Rwork0.205 --
all-15604 -
obs-15604 -
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 37 86 1590
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0233
X-RAY DIFFRACTIONc_angle_d1.479
X-RAY DIFFRACTIONc_mcbond_it1.268
X-RAY DIFFRACTIONc_mcangle_it2.195
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.47

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