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- PDB-4kyx: Crystal structure of ADP-ribose pyrophosphatase MutT from Rickett... -

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Basic information

Entry
Database: PDB / ID: 4kyx
TitleCrystal structure of ADP-ribose pyrophosphatase MutT from Rickettsia felis
ComponentsADP-ribose pyrophosphatase MutT
KeywordsHYDROLASE / ADP-ribose pyrophosphatase MutT / MutT / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / hydrolase activity
Similarity search - Function
NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADP-ribose pyrophosphatase MutT
Similarity search - Component
Biological speciesRickettsia felis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of ADP-ribose pyrophosphatase MutT from Rickettsia felis
Authors: Abendroth, J. / Clifton, M.C. / Lorimer, D. / Edwards, T.E.
History
DepositionMay 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribose pyrophosphatase MutT
B: ADP-ribose pyrophosphatase MutT


Theoretical massNumber of molelcules
Total (without water)35,0482
Polymers35,0482
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-15 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.980, 63.780, 71.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADP-ribose pyrophosphatase MutT


Mass: 17524.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia felis (bacteria) / Strain: ATCC VR-1525 / URRWXCal2 / Gene: mutT, RF_0595 / Plasmid: RifeA.17522.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q4ULX7, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.9737.7
2238.4
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2901vapor diffusion, sitting drop5.5JCSG screen, condition H10: 25% PEG 3350, 200mM ammonium acetate, 100mM BisTris pH 5.5; RifeA.17522.a.B1.PW36475 at 28.18 mg/ml, tray 241401h10; crystal incubated in 375mM NaI / 7.5% EG, and 750mM NaI / 15% EG; this crystal was used for phasing, VAPOR DIFFUSION, SITTING DROP, temperature 290K
2902vapor diffusion, sitting drop7.5JCSG screen, condition A5: 20% PEG 3350, 200mM magnesium formate; RifeA.17522.a.B1.PW36475 at 28.18 mg/ml, tray 241401a5; cryo: 10/20% EG; this crystal was used for refinement, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.5418
SYNCHROTRONAustralian Synchrotron MX120.9537
Detector
TypeIDDetectorDate
RIGAKU SATURN 944+1CCDApr 9, 2013
ADSC QUANTUM 210r2CCDMay 9, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1RIGAKU VARIMAXSINGLE WAVELENGTHMx-ray1
2Double Si with sagittaly bent second crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.95371
ReflectionNumber: 233954 / Rmerge(I) obs: 0.073 / D res high: 2.3 Å / Num. obs: 23577 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
2.32.36164091.210.457
2.362.42170399.910.278
2.422.49162310010.242
2.492.57164910010.211
2.572.66158210010.187
2.662.75152210010.153
2.752.85144210010.129
2.852.97140210010.104
2.973.1135410010.085
3.13.25128010010.07
3.253.43125399.810.057
3.433.64114499.810.064
3.643.89109299.610.058
3.894.2100098.210.041
4.24.692310010.033
4.65.1485710010.036
5.145.9474599.710.04
5.947.2762699.510.039
7.2710.2948398.410.032
ReflectionResolution: 1.8→50 Å / Num. all: 26627 / Num. obs: 26202 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 26.836 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 30.74
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.850.2616.971139018701,296
1.85-1.90.37.031315418011,297.1
1.9-1.950.13117.981234317581,295.3
1.95-2.010.14413.371243917011,295.6
2.01-2.080.10218.21281017391,299.9
2.08-2.150.08920.231238016861,299.9
2.15-2.230.08421.531177016061,299.3
2.23-2.320.06930.491018515381,298
2.32-2.430.0628.621090214911,299.8
2.43-2.550.05131.911058214501,2100
2.55-2.680.04436.09999213741,2100
2.68-2.850.03840.37937912961,299.9
2.85-3.040.03346.55879612331,2100
3.04-3.290.02952.57810511421,299.8
3.29-3.60.02756.79751010681,2100
3.6-4.020.02860.1565019691,299.6
4.02-4.650.02463.4355928471,298.9
4.65-5.690.02362.3147977361,299.2
5.69-8.050.02459.5337225931,299.2
8.05-500.02453.0414883041,284.4

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.3 Å / D res low: 35.53 Å / FOM : 0.452 / FOM acentric: 0.502 / FOM centric: 0.169 / Reflection: 12741 / Reflection acentric: 10832 / Reflection centric: 1831

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.8→46.5 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2436 / WRfactor Rwork: 0.2028 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.802 / SU B: 6.316 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1562 / SU Rfree: 0.1467 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 1291 4.9 %RANDOM
Rwork0.2128 ---
obs0.2149 24862 98.42 %-
all-26627 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.36 Å2 / Biso mean: 25.2832 Å2 / Biso min: 13.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 0 227 2407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192244
X-RAY DIFFRACTIONr_bond_other_d0.0010.022094
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.953052
X-RAY DIFFRACTIONr_angle_other_deg0.82434803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5265274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14525.259116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34815368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.677158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02538
X-RAY DIFFRACTIONr_mcbond_it1.0080.8951093
X-RAY DIFFRACTIONr_mcbond_other1.0010.8931092
X-RAY DIFFRACTIONr_mcangle_it1.7611.3311362
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 92 -
Rwork0.244 1775 -
all-1867 -
obs-1870 95.99 %
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)
12.55810.2088-0.01951.059-0.03710.65470.0916-0.0859-0.08630.0364-0.0626-0.0578-0.08220.0257-0.02910.0162-0.0021-0.00280.07360.01450.315140.20931.717-0.286
22.4777-0.3236-0.00760.8628-0.02810.46350.024-0.0037-0.05260.0044-0.0133-0.011-0.0146-0.0548-0.01070.01550.0038-0.00860.08430.00620.280611.27132.064-2.14
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 140
2X-RAY DIFFRACTION2B1 - 140

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