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- PDB-3crc: Crystal Structure of Escherichia coli MazG, the Regulator of Nutr... -

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Basic information

Entry
Database: PDB / ID: 3crc
TitleCrystal Structure of Escherichia coli MazG, the Regulator of Nutritional Stress Response
ComponentsProtein mazG
KeywordsHYDROLASE / tandem repeat domain
Function / homology
Function and homology information


ATP diphosphatase / TTP catabolic process / UTP catabolic process / dTTP catabolic process / nucleoside triphosphate diphosphatase activity / dATP catabolic process / ATP diphosphatase activity / dUTP catabolic process / dGTP catabolic process / cellular response to starvation ...ATP diphosphatase / TTP catabolic process / UTP catabolic process / dTTP catabolic process / nucleoside triphosphate diphosphatase activity / dATP catabolic process / ATP diphosphatase activity / dUTP catabolic process / dGTP catabolic process / cellular response to starvation / ATP binding / metal ion binding
Similarity search - Function
: / : / NTP pyrophosphohydrolase MazG / NTP pyrophosphohydrolase MazG, putative catalytic core / MazG nucleotide pyrophosphohydrolase domain / MazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Nucleoside triphosphate pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLee, S. / Kim, M.H. / Kang, B.S. / Kim, J.S. / Kim, Y.G. / Kim, K.J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of Escherichia coli MazG, the regulator of nutritional stress response.
Authors: Lee, S. / Kim, M.H. / Kang, B.S. / Kim, J.S. / Kim, G.H. / Kim, Y.G. / Kim, K.J.
History
DepositionApr 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Protein mazG
B: Protein mazG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7044
Polymers61,1732
Non-polymers5312
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-101.8 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.23, 66.91, 140.70
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein mazG / nucleotide pyrophosphohydrolase


Mass: 30586.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: mazG / Plasmid: pPROEX HTa / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P0AEY3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 49.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M trisodium citrate(pH 5.5), 0.2M ammonium acetate, 20% polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 15, 2007
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 12574 / Num. obs: 12574 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.076
Reflection shellResolution: 3→3.11 Å / Num. unique all: 12574 / Rsym value: 0.199

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→33.79 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.75 / SU B: 22.437 / SU ML: 0.44 / Cross valid method: THROUGHOUT / ESU R Free: 0.604 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3451 584 4.9 %RANDOM
Rwork0.21581 ---
obs0.22233 11405 93.86 %-
all-12574 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.569 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 3→33.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3613 0 32 13 3658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0410.0223690
X-RAY DIFFRACTIONr_angle_refined_deg3.7421.974983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.785439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96324.537205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.63515668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1931536
X-RAY DIFFRACTIONr_chiral_restr0.250.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022815
X-RAY DIFFRACTIONr_nbd_refined0.3870.22614
X-RAY DIFFRACTIONr_nbtor_refined0.3780.22509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2750.2279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3660.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.22
X-RAY DIFFRACTIONr_mcbond_it1.431.52309
X-RAY DIFFRACTIONr_mcangle_it2.35123548
X-RAY DIFFRACTIONr_scbond_it3.831590
X-RAY DIFFRACTIONr_scangle_it5.9864.51435
LS refinement shellResolution: 3→3.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 30 -
Rwork0.226 582 -
obs--67.11 %

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