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- PDB-2yf4: Crystal structure of DR2231, the MazG-like protein from Deinococc... -

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Basic information

Entry
Database: PDB / ID: 2yf4
TitleCrystal structure of DR2231, the MazG-like protein from Deinococcus radiodurans, Apo structure
ComponentsMAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
KeywordsHYDROLASE / DIMERIC DUTPASE
Function / homology
Function and homology information


nucleoside triphosphate diphosphatase activity / metal ion binding
Similarity search - Function
putative ntp pyrophosphohydrolase like fold / putative ntp pyrophosphohydrolase like domain / NTP pyrophosphohydrolase-like domain superfamily / Phosphoribosyl-ATP pyrophosphohydrolase-like / Phosphoribosyl-ATP pyrophosphohydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HAD superfamily Cof-like phosphohydrolase
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGoncalves, A.M.D. / deSanctis, D. / McSweeney, S.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Functional Insights Into Dr2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus Radiodurans.
Authors: Goncalves, A.M.D. / Desanctis, D. / Mcsweeney, S.M.
History
DepositionApr 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Version format compliance
Revision 1.2Jul 5, 2017Group: Refinement description / Category: software
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
B: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
C: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
D: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
E: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
F: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,10347
Polymers100,2526
Non-polymers3,85141
Water14,250791
1
A: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
B: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,83117
Polymers33,4172
Non-polymers1,41315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-149.3 kcal/mol
Surface area15940 Å2
MethodPISA
2
C: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
D: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,82317
Polymers33,4172
Non-polymers1,40515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-117 kcal/mol
Surface area16630 Å2
MethodPISA
3
E: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
F: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,45013
Polymers33,4172
Non-polymers1,03311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-106.9 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.778, 110.828, 166.110
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
MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE


Mass: 16708.691 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Plasmid: PET151/D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9RS96, nucleoside-triphosphate diphosphatase
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 2.85 Å3/Da / Density % sol: 56.47 % / Description: NONE
Crystal growDetails: 0.01M MAGNESIUM CHLORIDE,0.05M SODIUM CACODYLATE, PH 6.0, 1M LITHIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.24
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2009 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 137940 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 20.78 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 7.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YEU

2yeu


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.358 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 6916 5 %RANDOM
Rwork0.20876 ---
obs0.20993 130621 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.723 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2--0.93 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6804 0 227 791 7822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217143
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3892.0079702
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7395878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03623.174334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.501151084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9851578
X-RAY DIFFRACTIONr_chiral_restr0.0880.21072
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0225464
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7641.54452
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35127111
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.16532691
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.584.52591
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 527 -
Rwork0.265 9443 -
obs--99.53 %
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)
10.4973-0.1691-0.1340.78610.45431.88040.0230.0036-0.0738-0.0239-0.09210.03110.0812-0.19070.06910.00990.0045-0.00040.0805-0.02970.052318.265434.753815.1384
20.3289-0.1948-0.31620.99610.57622.2234-0.0366-0.01640.0656-0.0423-0.10340.128-0.1424-0.35940.13990.02590.0255-0.02820.1034-0.05430.067116.030839.797613.6541
31.40310.1902-0.39090.5849-0.19981.7211-0.0034-0.014-0.0489-0.0066-0.03670.05640.1275-0.07970.04010.02590.00320.02070.01420.00520.061945.833321.304640.9749
41.0517-0.0401-0.31630.55130.15871.10540.00630.02270.0094-0.0091-0.0139-0.07280.03960.10150.00760.03020.01260.02490.0210.02440.060751.24521.411941.9833
50.35820.1576-0.48581.1347-0.07452.19750.0116-0.1064-0.02070.3352-0.137-0.01690.07310.2060.12540.1564-0.06390.03130.08410.00730.075214.793141.299970.0312
60.76930.74740.10722.2960.23381.45330.2541-0.2231-0.07470.6226-0.32260.07110.2598-0.01890.06850.2172-0.110.0450.1185-0.00050.064811.289737.443968.2715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 22
2X-RAY DIFFRACTION1A23 - 144
3X-RAY DIFFRACTION2B-5 - 28
4X-RAY DIFFRACTION2B29 - 144
5X-RAY DIFFRACTION3C-4 - 28
6X-RAY DIFFRACTION3C29 - 144
7X-RAY DIFFRACTION4D-5 - 28
8X-RAY DIFFRACTION4D29 - 144
9X-RAY DIFFRACTION5E-4 - 31
10X-RAY DIFFRACTION5E32 - 143
11X-RAY DIFFRACTION6F-4 - 73
12X-RAY DIFFRACTION6F74 - 144

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