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- PDB-2yfd: STRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LI... -

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Database: PDB / ID: 2yfd
TitleSTRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE FROM DEINOCOCCUS RADIODURANS, COMPLEXED WITH Mg and dUMP
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
ACETATE ION / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / HAD superfamily Cof-like phosphohydrolase
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.767 Å
AuthorsGoncalves, A.M.D. / De Sanctis, 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 5, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Jan 25, 2017Group: Atomic model / Other
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,82915
Polymers66,8354
Non-polymers99511
Water6,900383
1
C: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
D: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9618
Polymers33,4172
Non-polymers5436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-82.3 kcal/mol
Surface area12240 Å2
MethodPISA
2
A: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
B: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8697
Polymers33,4172
Non-polymers4515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-79.7 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.090, 149.529, 52.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.997, 0.075, 0.008), (0.075, -0.997, -0.006), (0.007, 0.006, -1)
Vector: -3.0219, 78.28975, 26.07409)

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE / DR2231


Mass: 16708.691 Da / Num. of mol.: 4
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

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Non-polymers , 6 types, 394 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growDetails: 0.18 M LITHIUM ACETATE, 20% (W/V) PEG 3350, 10MM DUTP, 10MM MAGNESIUM CHLORIDE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 3, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.77→49.84 Å / Num. obs: 57356 / % possible obs: 94.3 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.2
Reflection shellResolution: 1.77→1.86 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.1 / % possible all: 75

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YF9

2yf9


Resolution: 1.767→19.934 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 19.53 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2114 2861 5 %
Rwork0.1843 --
obs0.1857 57235 93.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.881 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 22.06 Å2
Baniso -1Baniso -2Baniso -3
1-4.3761 Å20 Å20 Å2
2---1.2161 Å20 Å2
3----3.16 Å2
Refinement stepCycle: LAST / Resolution: 1.767→19.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 60 383 4549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014318
X-RAY DIFFRACTIONf_angle_d1.0585886
X-RAY DIFFRACTIONf_dihedral_angle_d15.3781655
X-RAY DIFFRACTIONf_chiral_restr0.073644
X-RAY DIFFRACTIONf_plane_restr0.005798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7669-1.79740.3721830.36251654X-RAY DIFFRACTION58
1.7974-1.830.34571200.28692134X-RAY DIFFRACTION75
1.83-1.86520.28711340.23652584X-RAY DIFFRACTION89
1.8652-1.90330.25451460.20642716X-RAY DIFFRACTION96
1.9033-1.94460.21281460.19382773X-RAY DIFFRACTION96
1.9446-1.98980.25121430.18612748X-RAY DIFFRACTION97
1.9898-2.03950.2341310.17452806X-RAY DIFFRACTION97
2.0395-2.09460.20231550.16542750X-RAY DIFFRACTION96
2.0946-2.15620.20611510.16172762X-RAY DIFFRACTION98
2.1562-2.22570.19851610.16272808X-RAY DIFFRACTION98
2.2257-2.30510.20441520.16712786X-RAY DIFFRACTION97
2.3051-2.39730.23321540.16892785X-RAY DIFFRACTION97
2.3973-2.50620.21261470.17272805X-RAY DIFFRACTION97
2.5062-2.6380.21951450.17982843X-RAY DIFFRACTION98
2.638-2.80290.19341560.18432816X-RAY DIFFRACTION98
2.8029-3.01860.20121410.17942877X-RAY DIFFRACTION98
3.0186-3.32110.22011500.18262851X-RAY DIFFRACTION97
3.3211-3.79880.17731300.17862896X-RAY DIFFRACTION98
3.7988-4.77520.17311490.16962940X-RAY DIFFRACTION98
4.7752-19.93520.21821670.21093040X-RAY DIFFRACTION98
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)
10.4886-0.5066-0.15270.7535-0.24670.7332-0.179-0.2303-0.09970.20730.06420.05830.24610.076200.16670.03650.00120.17390.03040.154716.545216.279213.1653
20.72060.2166-0.42331.4137-0.99242.0127-0.0679-0.0655-0.06730.14080.0443-0.0005-0.0208-0.0295-0.00020.02340.007-0.02280.07370.00160.042214.787628.02260.0703
30.3292-0.1418-0.03730.813-0.56430.50720.03010.1763-0.2586-0.42770.14390.36560.2654-0.2519-0.0110.1023-0.0307-0.02610.16470.00940.15377.206824.6801-9.4119
40.733-0.2259-0.37261.2805-0.36821.973-0.0559-0.0474-0.0743-0.02020.0102-0.13010.16430.0694-0.0011-0.0210.0227-0.020.05390.02090.082919.134121.94511.3114
50.43320.42150.23580.49630.07020.6736-0.06970.11930.1542-0.27750.05170.0391-0.61980.034-0.00020.3267-0.00170.02450.1350.0250.16614.775963.203813.1218
60.8631-0.16010.41161.874-0.84532.3601-0.04210.00650.0355-0.01510.0347-0.0404-0.1993-0.0329-0.00010.03610.02580.0290.029-0.00430.036714.045951.695426.4375
70.3720.0260.00550.2065-0.22330.2363-0.0009-0.32050.17210.50590.13250.221-0.4674-0.3648-0.00240.21170.07050.04370.16490.0030.14516.047554.199635.6119
80.62110.02330.14691.5348-0.68781.755-0.04810.00110.07020.10560.0083-0.1578-0.37890.0976-0.00150.0709-0.01160.01040.05090.01050.103217.816757.065924.9829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:45)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 46:144)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 7:28)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 29:145)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 7:45)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 46:143)
7X-RAY DIFFRACTION7(CHAIN D AND RESID 7:28)
8X-RAY DIFFRACTION8(CHAIN D AND RESID 29:144)

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