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- PDB-1z2z: Crystal Structure of the Putative tRNA pseudouridine synthase D (... -

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Basic information

Entry
Database: PDB / ID: 1z2z
TitleCrystal Structure of the Putative tRNA pseudouridine synthase D (TruD) from Methanosarcina mazei, Northeast Structural Genomics Target MaR1
ComponentsProbable tRNA pseudouridine synthase D
KeywordsLYASE / alpha-beta protein. / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


tRNA pseudouridine13 synthase / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / RNA binding
Similarity search - Function
Hypothetical Protein Yqey; Chain: A; domain1 - #30 / Alpha-Beta Plaits - #3160 / TruD, catalytic domain / Pseudouridine synthase TruD, conserved site / tRNA pseudouridine synthase D (TruD) / Uncharacterized protein family UPF0024 signature. / Pseudouridine synthase, TruD, insertion domain / TRUD domain profile. / Pseudouridine synthase, TruD, catalytic domain / Pseudouridine synthase, TruD ...Hypothetical Protein Yqey; Chain: A; domain1 - #30 / Alpha-Beta Plaits - #3160 / TruD, catalytic domain / Pseudouridine synthase TruD, conserved site / tRNA pseudouridine synthase D (TruD) / Uncharacterized protein family UPF0024 signature. / Pseudouridine synthase, TruD, insertion domain / TRUD domain profile. / Pseudouridine synthase, TruD, catalytic domain / Pseudouridine synthase, TruD / Hypothetical Protein Yqey; Chain: A; domain1 / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Probable tRNA pseudouridine synthase D
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsForouhar, F. / Yong, W. / Ciano, M. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Putative tRNA pseudouridine synthase D (TruD) from Methanosarcina mazei, Northeast Structural Genomics Target MaR1
Authors: Forouhar, F. / Yong, W. / Ciano, M. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable tRNA pseudouridine synthase D
B: Probable tRNA pseudouridine synthase D


Theoretical massNumber of molelcules
Total (without water)102,1152
Polymers102,1152
Non-polymers00
Water3,963220
1
A: Probable tRNA pseudouridine synthase D


Theoretical massNumber of molelcules
Total (without water)51,0581
Polymers51,0581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable tRNA pseudouridine synthase D


Theoretical massNumber of molelcules
Total (without water)51,0581
Polymers51,0581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.562, 132.531, 66.779
Angle α, β, γ (deg.)90.00, 116.98, 90.00
Int Tables number4
Space group name H-MP1211
Detailspossibly monomer.

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Components

#1: Protein Probable tRNA pseudouridine synthase D / Pseudouridylate synthase / Uracil hydrolyase


Mass: 51057.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: truD / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic
Keywords: TruD, Substitution of Met residues by Seleno-Met residues and addition of C-tag (LEHHHHHH).
References: UniProt: Q8Q0M2, pseudouridylate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate acid (pH 6.5), 16% PEG 8k, 200 mM magnesium acetate, and 5 mM DTT. , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97931 / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 6, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 58645 / Num. obs: 58176 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.051 / Net I/σ(I): 23.62
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 5.4 / Num. unique all: 5755 / Rsym value: 0.219 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.03 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 214565.63 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: XtalView was also used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.296 5280 9.9 %RANDOM
Rwork0.233 ---
all0.236 58176 --
obs0.233 53409 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.4917 Å2 / ksol: 0.289214 e/Å3
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1-14.49 Å20 Å23.65 Å2
2---2.11 Å20 Å2
3----12.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6956 0 0 220 7176
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 735 9.9 %
Rwork0.321 6722 -
obs-6722 76.3 %

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