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- PDB-2yf3: Crystal structure of DR2231, the MazG-like protein from Deinococc... -

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Basic information

Entry
Database: PDB / ID: 2yf3
TitleCrystal structure of DR2231, the MazG-like protein from Deinococcus radiodurans, complex with manganese
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: 2 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: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_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_asym_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
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)104,96461
Polymers100,2526
Non-polymers4,71255
Water14,394799
1
A: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
B: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,98720
Polymers33,4172
Non-polymers1,57018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-131.7 kcal/mol
Surface area16690 Å2
MethodPISA
2
C: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
D: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,40725
Polymers33,4172
Non-polymers1,98923
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-108.5 kcal/mol
Surface area17480 Å2
MethodPISA
3
E: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
F: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,57016
Polymers33,4172
Non-polymers1,15314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-102 kcal/mol
Surface area16890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.109, 111.402, 166.539
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 799 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.84 Å3/Da / Density % sol: 56.03 % / Description: NONE
Crystal growDetails: 0.01M MAGNESIUM CHLORIDE, 0.05M SODIUM CACODYLATE, PH 6.0, 1M LITHIUM SULFATE. OVERNIGHT SOAK IN 250MM LITHIUM SULFATE / 750MM MANGANESE SULFATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2009 / Details: PT COATED MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 86122 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 19.167 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15
Reflection shellResolution: 2→2.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 6.8 / % possible all: 100

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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: 2→43.12 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.522 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23834 4239 4.9 %RANDOM
Rwork0.19144 ---
obs0.19374 81820 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.643 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--0.94 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 2→43.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6936 0 261 799 7996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227299
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5252.0079905
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.075898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75123.294340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.326151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2411578
X-RAY DIFFRACTIONr_chiral_restr0.1020.21099
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0225588
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_it0.8171.54555
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4127278
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.50732744
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8854.52627
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: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 310 -
Rwork0.214 5954 -
obs--100 %
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)
10.6133-0.1052-0.24970.58670.35282.2902-0.00660.024-0.1229-0.0065-0.08750.05530.2474-0.25680.09410.0429-0.03890.0050.0951-0.02640.075318.273335.04215.1333
20.7332-0.2591-0.08421.05940.78033.7044-0.0667-0.03610.0335-0.0303-0.13050.17710.0102-0.53290.19720.0231-0.0134-0.00530.1068-0.05060.06415.749839.949813.9508
31.36680.0783-0.34470.8266-0.20061.7933-0.02090.0619-0.1255-0.0098-0.03820.03390.2181-0.08150.05920.0316-0.00640.01650.0112-0.00020.059545.727720.700841.3254
41.1604-0.0033-0.27630.7678-0.09111.4521-0.00930.0402-0.0625-0.0561-0.0583-0.14590.13010.13680.06760.03510.01540.02430.02290.02230.072851.59721.175841.6759
50.53040.0233-0.65840.99860.02883.1516-0.0604-0.0858-0.07330.2659-0.1222-0.06980.18070.40190.18270.133-0.03250.03010.0980.02110.094615.819641.271969.976
60.75510.3964-0.11591.66010.64091.88490.0908-0.1772-0.13510.507-0.21960.05290.39150.08710.12880.1963-0.06180.05920.12330.00980.089711.623637.576868.6662
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 21
2X-RAY DIFFRACTION1A22 - 144
3X-RAY DIFFRACTION2B-4 - 5
4X-RAY DIFFRACTION2B6 - 147
5X-RAY DIFFRACTION3C-4 - 3
6X-RAY DIFFRACTION3C4 - 148
7X-RAY DIFFRACTION4D-5 - 24
8X-RAY DIFFRACTION4D25 - 147
9X-RAY DIFFRACTION5E-4 - 24
10X-RAY DIFFRACTION5E25 - 148
11X-RAY DIFFRACTION6F-3 - 7
12X-RAY DIFFRACTION6F8 - 144

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