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

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Database: PDB / ID: 2yfc
TitleSTRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE FROM DEINOCOCCUS RADIODURANS, COMPLEXED WITH Mn 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
: / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / HAD superfamily Cof-like phosphohydrolase
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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 1.1Sep 7, 2011Group: Database references / Non-polymer description / Version format compliance
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_asym_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_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,14916
Polymers66,8354
Non-polymers1,31412
Water5,657314
1
A: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
B: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0758
Polymers33,4172
Non-polymers6576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-70.6 kcal/mol
Surface area12520 Å2
MethodPISA
2
C: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
D: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0758
Polymers33,4172
Non-polymers6576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-71.5 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.733, 150.191, 52.423
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: (0.99739, 0.07189, 0.00614), (0.07192, -0.9974, -0.00492), (0.00577, 0.00534, -0.99997)
Vector: 2.4283, -68.58492, 26.72167)

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Components

#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
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 49.95 % / Description: NONE
Crystal growDetails: 0.18 M LITHIUM ACETATE AND 20% (W/V) PEG 3350, 10MM DUTP AND 10 MM MANGANESE CHLORIDE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 48355 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 20.29 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / % possible all: 93.4

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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: 2.01→20.001 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 2082 5 %
Rwork0.1775 --
obs0.1796 41628 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.377 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso mean: 24.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.6835 Å20 Å20 Å2
2---0.3526 Å20 Å2
3----0.1906 Å2
Refinement stepCycle: LAST / Resolution: 2.01→20.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4096 0 70 314 4480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124263
X-RAY DIFFRACTIONf_angle_d1.1515804
X-RAY DIFFRACTIONf_dihedral_angle_d15.0791623
X-RAY DIFFRACTIONf_chiral_restr0.069639
X-RAY DIFFRACTIONf_plane_restr0.005780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.05670.25321360.18792574X-RAY DIFFRACTION98
2.0567-2.10810.21551360.16672607X-RAY DIFFRACTION99
2.1081-2.1650.20841370.15882585X-RAY DIFFRACTION99
2.165-2.22870.2361370.15952602X-RAY DIFFRACTION99
2.2287-2.30050.21471380.16132635X-RAY DIFFRACTION99
2.3005-2.38260.21481400.1642654X-RAY DIFFRACTION99
2.3826-2.47780.24341380.17282605X-RAY DIFFRACTION99
2.4778-2.59040.26351370.18562615X-RAY DIFFRACTION99
2.5904-2.72660.27181400.18972657X-RAY DIFFRACTION100
2.7266-2.8970.2461400.19142658X-RAY DIFFRACTION100
2.897-3.11990.21271400.1942679X-RAY DIFFRACTION100
3.1199-3.43240.22861410.18352664X-RAY DIFFRACTION100
3.4324-3.92590.1791420.17162709X-RAY DIFFRACTION100
3.9259-4.93390.20371420.15862671X-RAY DIFFRACTION98
4.9339-20.00180.19641380.19892631X-RAY DIFFRACTION92
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)
10.5008-0.1851-0.10040.7198-0.42330.3446-0.1732-0.1542-0.0414-0.04980.00820.00040.13440.09830.10360.17860.03220.01320.15520.02010.1532-22.6612-58.895613.2917
20.16560.1320.06140.4299-0.5590.8289-0.0638-0.0279-0.03190.0760.0481-0.04-0.0067-0.02710.01120.0720.03360.00860.12170.01710.1057-24.3326-47.35630.1675
30.3885-0.328-0.15270.52550.4120.68360.07160.1831-0.2153-0.2078-0.00070.23930.0146-0.1084-0.04390.1229-0.0378-0.01340.1410.02720.1318-31.9262-50.3673-9.5722
40.04130.0157-0.10230.5338-0.15910.5506-0.0572-0.0309-0.0286-0.0104-0.0122-0.07710.13940.00720.01090.09590.02910.01140.08190.0120.086-20.1297-53.05771.3258
50.20840.23520.02550.3223-0.01130.5723-0.11180.06810.1859-0.16810.0155-0.0783-0.48130.0910.04320.26590.0155-0.00690.10990.03870.1673-24.3554-11.45912.9564
60.1345-0.1371-0.05480.7831-0.40710.9449-0.0089-0.03620.0076-0.0240.0085-0.0161-0.0962-0.0602-0.00470.06450.0063-0.01030.07820.01090.0739-24.9976-23.121926.4354
70.19980.1004-0.19510.81890.150.3096-0.0321-0.14990.14350.20170.07270.2698-0.0451-0.18960.01990.12990.06710.02960.13590.00430.1216-32.9728-20.750835.8615
80.1453-0.02430.18440.7498-0.28550.444-0.05890.0190.03760.0708-0.0041-0.0908-0.23290.07750.04560.115-0.0109-0.01060.0620.00830.1009-21.2774-17.19625.2073
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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