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- PDB-3qsj: Crystal structure of NUDIX hydrolase from Alicyclobacillus acidoc... -

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Basic information

Entry
Database: PDB / ID: 3qsj
TitleCrystal structure of NUDIX hydrolase from Alicyclobacillus acidocaldarius
ComponentsNUDIX hydrolase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
Acyl-coenzyme A diphosphatase NUDT19 / 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
Biological speciesAlicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsMichalska, K. / Wu, R. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of NUDIX hydrolase from Alicyclobacillus acidocaldarius
Authors: Michalska, K. / Wu, R. / Bearden, J. / Joachimiak, A.
History
DepositionFeb 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUDIX hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4285
Polymers25,1121
Non-polymers3164
Water3,423190
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.844, 82.152, 36.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein NUDIX hydrolase


Mass: 25111.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
Strain: DSM 446 / Gene: Aaci_1025 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: C8WVE1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M CaCl2, 0.1 M Tris/HCl, 23% PEG4K, 5% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 25693 / Num. obs: 25239 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 23.52 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 25.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.2 / % possible all: 95.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
PHENIXrefinement
BUSTER2.8.0refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→37.42 Å / Cor.coef. Fo:Fc: 0.9426 / Cor.coef. Fo:Fc free: 0.9342 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 1282 5.1 %RANDOM
Rwork0.1747 ---
obs0.1762 25138 97.8 %-
all-25138 --
Displacement parametersBiso mean: 26.68 Å2
Baniso -1Baniso -2Baniso -3
1-5.9529 Å20 Å20 Å2
2---4.1371 Å20 Å2
3----1.8158 Å2
Refine analyzeLuzzati coordinate error obs: 0.181 Å
Refinement stepCycle: LAST / Resolution: 1.7→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 19 190 1878
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0141804HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.182460HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d622SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes273HARMONIC5
X-RAY DIFFRACTIONt_it1804HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.13
X-RAY DIFFRACTIONt_other_torsion14.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion238SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2259SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.77 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.242 142 5.17 %
Rwork0.1997 2602 -
all0.2019 2744 -
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)
10.3491-0.45950.09651.089-0.24713.21360.01720.0465-0.0662-0.01940.01930.13110.1463-0.2784-0.0364-0.0503-0.00830.00010.0206-0.0021-0.03255.61658.120325.3937
22.991-0.4749-0.07490.29150.18620.5576-0.05250.08650.1921-0.05610.01380.003-0.1164-0.11430.0386-0.00940.0206-0.01230.0191-0.0018-0.010358.43115.563318.9754
31.4359-0.6510.03130.73840.02721.3603-0.0314-0.00130.24820.00810.0082-0.1303-0.1113-0.02330.0232-0.03310.0023-0.0088-0.03610.0084-0.007867.941616.058323.5582
41.1012-0.21510.32391.29860.3020.59450.07360.02310.0948-0.0281-0.06720.1015-0.0522-0.0597-0.0064-0.03030.0180.0034-0.01380.0009-0.041162.7599.943619.247
53.5688-0.44810.99872.5006-0.13631.2953-0.1339-0.34190.15060.2620.15280.0065-0.109-0.2052-0.0189-0.01590.03340.01080.0674-0.0126-0.049156.787513.742633.8564
62.4609-1.8760.16831.79580.07031.84150.0261-0.0278-0.54420.05210.0570.44010.2846-0.363-0.0832-0.0606-0.0528-0.0002-0.00940.02710.02852.6534-0.22727.2522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|0 - A|28}A0 - 28
2X-RAY DIFFRACTION2{A|29 - A|60}A29 - 60
3X-RAY DIFFRACTION3{A|61 - A|115}A61 - 115
4X-RAY DIFFRACTION4{A|116 - A|159}A116 - 159
5X-RAY DIFFRACTION5{A|160 - A|181}A160 - 181
6X-RAY DIFFRACTION6{A|182 - A|221}A182 - 221

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