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- PDB-1okj: crystal structure of the essential E. coli YeaZ protein by MAD me... -

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Basic information

Entry
Database: PDB / ID: 1okj
Titlecrystal structure of the essential E. coli YeaZ protein by MAD method using the gadolinium complex "DOTMA"
ComponentsTRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB
KeywordsHYDROLASE / POTENTIAL ZINC PROTEASE / HYPOTHETICAL PROTEASE YEAZ / METALLOPROTEASE / BACTERIAL TARGETS AT IGS-CNRS / FRANCE / BIGS / STRUCTURAL GENOMICS
Function / homology
Function and homology information


EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / maintenance of translational fidelity / metallopeptidase activity / identical protein binding / cytosol
Similarity search - Function
tRNA threonylcarbamoyl adenosine modification protein TsaB / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GADOLINIUM ION / tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.28 Å
AuthorsAbergel, C. / Jeudy, S. / Claverie, J.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: A Complement to the Modern Crystallographer'S Toolbox: Caged Gadolinium Complexes with Versatile Binding Modes.
Authors: Stelter, M. / Molina, R. / Jeudy, S. / Kahn, R. / Abergel, C. / Hermoso, J.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Preliminary Crystallographic Analysis of the Escherichia Coli Yeaz Protein Using the Anomalous Signal of a Gadolinium Derivative.
Authors: Jeudy, S. / Stelter, M. / Coutard, B. / Kahn, R. / Abergel, C.
History
DepositionJul 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jul 23, 2014Group: Database references / Other / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB
B: TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB
C: TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB
D: TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,69612
Polymers110,4384
Non-polymers1,2588
Water5,459303
1
A: TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB
B: TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,47710
Polymers55,2192
Non-polymers1,2588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-22.7 kcal/mol
Surface area19190 Å2
MethodPISA
2
C: TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB
D: TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB


Theoretical massNumber of molelcules
Total (without water)55,2192
Polymers55,2192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-22.9 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.340, 97.600, 141.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB / HYPOTHETICAL PROTEASE YEAZ / T(6)A37 THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB


Mass: 27609.381 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: GATEWAY PEPTIDE INSERTED ON THE PROTEIN SEQUENCE FOR PROTEIN EXPRESSION AND PURIFICATION
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P76256, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical
ChemComp-GD3 / GADOLINIUM ION / Gadolinium


Mass: 157.250 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Gd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL INSERTION OF THE GATEWAY PEPTIDE

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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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growpH: 4.7
Details: PEG 8000, NA ACETATE 0.1M PH 4.7, NACL 0.2M, GLYCEROL 10%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.71058
DetectorDate: Jun 15, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.71058 Å / Relative weight: 1
ReflectionResolution: 2.28→19.85 Å / Num. obs: 48235 / % possible obs: 98.3 % / Redundancy: 5 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 11
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 1.9 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
autoSHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.28→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: 14 C-TERMINUS RESIDUES AND 20 GATEWAY N-TERMINUS RESIDUES DISORDERED IN THE 4 MOLECULES OF THE AU
RfactorNum. reflection% reflectionSelection details
Rfree0.257 4871 10.1 %RANDOM
Rwork0.216 ---
obs0.216 48235 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.5533 Å2 / ksol: 0.359104 e/Å3
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.03 Å20 Å20 Å2
2---3.35 Å20 Å2
3----0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.28→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6672 0 8 303 6983
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.172.5
LS refinement shellResolution: 2.28→2.42 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 731 10 %
Rwork0.254 6613 -
obs--91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMWATER.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMGD.TOPPAR
X-RAY DIFFRACTION3GD.PARAM
X-RAY DIFFRACTION4PROTEIN.TOP

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