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- PDB-6wwd: Crystal structure of Nucleoside-triphosphatase / dITP/XTP pyropho... -

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Basic information

Entry
Database: PDB / ID: 6wwd
TitleCrystal structure of Nucleoside-triphosphatase / dITP/XTP pyrophosphatase from Mycobacterium abscessus ATCC 19977 / DSM 44196
ComponentsdITP/XTP pyrophosphatase
KeywordsHYDROLASE / SSGCID / Nucleoside-triphosphatase / dITP/XTP pyrophosphatase / Mycobacterium abscessus / Mycobacteroides abscessus / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding / metal ion binding
Similarity search - Function
dITP/XTP pyrophosphatase / Ham1-like protein / Ham1 family / Maf protein - #10 / Inosine triphosphate pyrophosphatase-like / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
dITP/XTP pyrophosphatase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Nucleoside-triphosphatase / dITP/XTP pyrophosphatase from Mycobacterium abscessus ATCC 19977 / DSM 44196
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMay 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dITP/XTP pyrophosphatase
B: dITP/XTP pyrophosphatase
C: dITP/XTP pyrophosphatase
D: dITP/XTP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)90,8074
Polymers90,8074
Non-polymers00
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12260 Å2
ΔGint-90 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.690, 104.040, 146.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 through 2 and (name N...
21(chain B and ((resid 1 through 2 and (name N...
31(chain C and (resid 1 through 20 or (resid 21...
41(chain D and ((resid 1 through 2 and (name N...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYS(chain A and ((resid 1 through 2 and (name N...AA1 - 21 - 2
12METMETARGARG(chain A and ((resid 1 through 2 and (name N...AA1 - 1961 - 196
13METMETARGARG(chain A and ((resid 1 through 2 and (name N...AA1 - 1961 - 196
14METMETARGARG(chain A and ((resid 1 through 2 and (name N...AA1 - 1961 - 196
15METMETARGARG(chain A and ((resid 1 through 2 and (name N...AA1 - 1961 - 196
21METMETLYSLYS(chain B and ((resid 1 through 2 and (name N...BB1 - 21 - 2
22METMETMETMET(chain B and ((resid 1 through 2 and (name N...BB1 - 1941 - 194
23METMETMETMET(chain B and ((resid 1 through 2 and (name N...BB1 - 1941 - 194
24METMETMETMET(chain B and ((resid 1 through 2 and (name N...BB1 - 1941 - 194
25METMETMETMET(chain B and ((resid 1 through 2 and (name N...BB1 - 1941 - 194
31METMETLEULEU(chain C and (resid 1 through 20 or (resid 21...CC1 - 201 - 20
32GLUGLUGLUGLU(chain C and (resid 1 through 20 or (resid 21...CC2121
33METMETGLYGLY(chain C and (resid 1 through 20 or (resid 21...CC1 - 2021 - 202
41METMETLYSLYS(chain D and ((resid 1 through 2 and (name N...DD1 - 21 - 2
42METMETARGARG(chain D and ((resid 1 through 2 and (name N...DD1 - 2031 - 203
43METMETARGARG(chain D and ((resid 1 through 2 and (name N...DD1 - 2031 - 203
44METMETARGARG(chain D and ((resid 1 through 2 and (name N...DD1 - 2031 - 203
45METMETARGARG(chain D and ((resid 1 through 2 and (name N...DD1 - 2031 - 203

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Components

#1: Protein
dITP/XTP pyrophosphatase / Non-canonical purine NTP pyrophosphatase / Non-standard purine NTP pyrophosphatase / Nucleoside- ...Non-canonical purine NTP pyrophosphatase / Non-standard purine NTP pyrophosphatase / Nucleoside-triphosphate diphosphatase / Nucleoside-triphosphate pyrophosphatase / NTPase


Mass: 22701.645 Da / Num. of mol.: 4 / Fragment: MyabA.00786.a.AE1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria)
Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543
Gene: MAB_1485 / Plasmid: MyabA.00786.a.AE1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: B1MLZ4, XTP/dITP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: RigakuReagents, JCSG+ screen, condition a2: 20% PEG 3000, 100mM sodium citrate tribasic / citric acid pH 5.5: MyabA.00786.a.AE1.PS38631 at 26.62 mg/ml: tray 315036 a2, cryo: 20% ethylene ...Details: RigakuReagents, JCSG+ screen, condition a2: 20% PEG 3000, 100mM sodium citrate tribasic / citric acid pH 5.5: MyabA.00786.a.AE1.PS38631 at 26.62 mg/ml: tray 315036 a2, cryo: 20% ethylene glycol, puck rse0-4. For phasing, a crystal from the same well was soaked for 20sec in a solution made of 20% 2.5M sodium iodide in ethylene glycol and 80% reservoir, and then vitrified in liquid nitrogen: tray 315056 a2, puck fdv5-14

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 22, 2020 / Details: RIGAKU VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→47.9 Å / Num. obs: 45678 / % possible obs: 99.1 % / Redundancy: 7.031 % / Biso Wilson estimate: 26.991 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.126 / Χ2: 0.876 / Net I/σ(I): 14.47 / Num. measured all: 321160 / Scaling rejects: 24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.156.0820.4114.6219792332032540.8910.4598
2.15-2.217.0190.3725.5222509329932070.9350.40297.2
2.21-2.286.5940.4015.8920863319431640.9440.43699.1
2.28-2.357.3030.3396.1321945306330050.9560.36598.1
2.35-2.427.2550.3146.6821749305329980.960.33898.2
2.42-2.517.2350.297.1220859288928830.9690.31299.8
2.51-2.67.3060.2697.3920252280627720.9720.2998.8
2.6-2.717.1510.2359.1119308272927000.9780.25398.9
2.71-2.837.2460.18510.4218761261025890.9860.19999.2
2.83-2.977.250.15712.2218175251025070.9910.16999.9
2.97-3.137.2830.12315.217079235623450.9950.13399.5
3.13-3.327.280.08919.7816321225022420.9970.09699.6
3.32-3.557.0620.07924.3115020213121270.9970.08599.8
3.55-3.836.9420.06727.8313836199719930.9980.07299.8
3.83-4.26.8250.05531.1612599184618460.9990.06100
4.2-4.77.1710.04336.0811975167016700.9990.046100
4.7-5.427.1140.05329.3910642149614960.9990.058100
5.42-6.647.0130.06225.148927127312730.9990.067100
6.64-9.396.8310.04135.686899101110100.9990.04499.9
9.39-47.96.1120.02652.29364960759710.02898.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18refinement
PDB_EXTRACT3.25data extraction
SHELXDEphasing
PHASERphasing
ARP/wARPmodel building
Cootmodel building
PARROTphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→47.9 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 1961 4.29 %0
Rwork0.1861 43703 --
obs0.1885 45664 99.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.57 Å2 / Biso mean: 30.1091 Å2 / Biso min: 8.84 Å2
Refinement stepCycle: final / Resolution: 2.1→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5518 0 0 550 6068
Biso mean---28.01 -
Num. residues----776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075693
X-RAY DIFFRACTIONf_angle_d0.9327779
X-RAY DIFFRACTIONf_chiral_restr0.056921
X-RAY DIFFRACTIONf_plane_restr0.0061030
X-RAY DIFFRACTIONf_dihedral_angle_d18.8162032
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2865X-RAY DIFFRACTION8.973TORSIONAL
12B2865X-RAY DIFFRACTION8.973TORSIONAL
13C2865X-RAY DIFFRACTION8.973TORSIONAL
14D2865X-RAY DIFFRACTION8.973TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.25481300.21233012314298
2.15-2.210.25451440.20443018316297
2.21-2.280.31871500.25683062321299
2.28-2.350.28461340.20963034316898
2.35-2.430.27351280.20643074320298
2.43-2.530.26261360.20383110324699
2.53-2.650.28171430.200131023245100
2.65-2.790.261440.20253092323699
2.79-2.960.27971220.18583151327399
2.96-3.190.23941280.18473137326599
3.19-3.510.2191680.166531283296100
3.51-4.020.20451370.15831843321100
4.02-5.060.21221580.148832193377100
5.06-47.90.23021390.195733803519100
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)
11.29731.65121.65021.89841.01261.4632-0.10150.08110.0346-0.09250.02270.2074-0.12390.0120.04550.14880.00260.00890.1730.01580.084436.29416.79198.4203
21.885-0.64430.07481.19460.45891.3239-0.05920.3885-0.2329-0.04480.2772-0.1982-0.06310.3539-0.19850.119-0.01230.00340.15470.03920.045643.649311.51759.0923
32.78932.1148-0.38162.85550.03190.0262-0.03030.1638-0.0741-0.08770.1347-0.167-0.03740.0183-0.10040.1354-0.00320.01050.20940.02650.09150.819516.84412.9691
40.55382.0058-1.11358.313-3.62491.76020.1642-0.12770.3102-1.1907-0.19481.52560.42680.2671-0.10290.62260.1497-0.16860.6921-0.0290.525947.78514.6114-4.3936
56.3162-4.1259-0.34163.0009-0.19763.4605-0.19581.9217-1.9892-1.08770.62280.19940.5275-0.0854-0.16660.5125-0.22140.03660.5435-0.21480.604354.6712-9.675-4.3788
62.23741.8859-2.47250.706-0.98032.07-0.0916-0.0721-0.1529-0.0140.022-0.20110.15290.1730.05060.15060.019-0.02390.1780.01280.167251.3622-6.448513.6478
71.51490.06960.03911.2162-0.47691.53530.02780.0781-0.1745-0.07760.11110.09890.2719-0.2389-0.1180.1512-0.0156-0.05070.11940.00010.148835.7738-9.038913.0208
84.378-0.37431.75530.48981.06113.823-0.52330.7761-0.66410.06020.5522-0.5493-0.1071.04440.02270.43260.098-0.05531.17380.06550.573234.98350.5165-4.1124
95.3737-1.696-0.7344.93911.95644.77440.0383-0.9543-0.25780.508-0.00040.1920.3304-0.0774-0.00590.1834-0.067-0.01670.25130.02590.175855.148924.335247.8061
104.04620.56472.96370.66740.27742.0648-0.00820.34330.0399-0.0181-0.0011-0.1626-0.00810.170.03090.13750.00580.02510.1296-0.01390.133554.237618.913332.3962
114.4119-1.0709-1.34494.8854-1.86464.08810.10520.23030.21770.1035-0.00890.0436-0.3748-0.1854-0.06030.19920.00820.02440.1027-0.00040.062837.733925.848321.328
125.2003-2.08081.21722.4342-0.58461.85720.082-0.22040.0446-0.06230.05880.025-0.0964-0.2014-0.12130.1292-0.00760.02630.06530.00490.043639.741421.150133.9544
130.97280.0273-0.22910.37060.12081.75420.1565-1.0172-0.13240.6446-0.31860.41750.30450.2969-0.08860.4623-0.01730.07970.56840.13450.338631.544320.292443.2209
146.87521.92422.25863.75060.7715.09780.1458-1.0866-0.04190.8352-0.3443-0.55060.0141-0.06940.07970.3454-0.0348-0.10920.43920.14560.369428.54827.362253.3825
151.5818-2.135-1.00071.97181.22451.1956-0.06660.0287-0.21320.08530.01550.31190.0909-0.17040.04260.1351-0.0376-0.0160.16340.02350.175232.7478-0.202135.9792
162.3314-0.94140.61852.0133-0.31670.408-0.0732-0.2032-0.05810.14650.1732-0.23090.02330.0293-0.08360.1411-0.015-0.03230.10950.02530.129548.4168-2.030237.4924
173.4124-3.02462.82544.8599-2.51353.8562-0.7248-0.2227-0.07661.15180.42370.4551-0.7984-0.56160.34270.5431-0.04980.06870.5893-0.07070.409247.177810.886747.6534
184.81993.13260.06213.7358-2.14113.8146-0.2130.789-0.4481-0.84970.3406-0.71540.5309-0.0244-0.01610.4028-0.001-0.00950.339-0.00950.328229.425710.3347-8.4226
193.20741.6523.19521.5380.96294.3258-0.06780.06260.263-0.67570.14990.2309-0.0502-0.47960.1960.4378-0.0055-0.10420.34170.08350.22625.154412.1573-0.7002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 49 through 108 )B49 - 108
2X-RAY DIFFRACTION2chain 'B' and (resid 109 through 133 )B109 - 133
3X-RAY DIFFRACTION3chain 'B' and (resid 134 through 174 )B134 - 174
4X-RAY DIFFRACTION4chain 'B' and (resid 175 through 194 )B175 - 194
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 35 )C1 - 35
6X-RAY DIFFRACTION6chain 'C' and (resid 36 through 97 )C36 - 97
7X-RAY DIFFRACTION7chain 'C' and (resid 98 through 183 )C98 - 183
8X-RAY DIFFRACTION8chain 'C' and (resid 184 through 202 )C184 - 202
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 36 )D1 - 36
10X-RAY DIFFRACTION10chain 'D' and (resid 37 through 80 )D37 - 80
11X-RAY DIFFRACTION11chain 'D' and (resid 81 through 117 )D81 - 117
12X-RAY DIFFRACTION12chain 'D' and (resid 118 through 163 )D118 - 163
13X-RAY DIFFRACTION13chain 'D' and (resid 164 through 203 )D164 - 203
14X-RAY DIFFRACTION14chain 'A' and (resid 1 through 35 )A1 - 35
15X-RAY DIFFRACTION15chain 'A' and (resid 36 through 97 )A36 - 97
16X-RAY DIFFRACTION16chain 'A' and (resid 98 through 174 )A98 - 174
17X-RAY DIFFRACTION17chain 'A' and (resid 175 through 196 )A175 - 196
18X-RAY DIFFRACTION18chain 'B' and (resid 1 through 20 )B1 - 20
19X-RAY DIFFRACTION19chain 'B' and (resid 21 through 48 )B21 - 48

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