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- PDB-2wfe: Structure of the Candida albicans cytosolic leucyl-tRNA synthetas... -

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Basic information

Entry
Database: PDB / ID: 2wfe
TitleStructure of the Candida albicans cytosolic leucyl-tRNA synthetase editing domain
ComponentsCYTOSOLIC LEUCYL-TRNA SYNTHETASE
KeywordsLIGASE / LEUCYL-TRNA SYNTHETASE / EDITING DOMAIN / CANDIDA ALBICANS / HYDROLYSIS OF MIS-CHARGED TRNAS
Function / homologyIsoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Alpha-Beta Complex / Alpha Beta / :
Function and homology information
Biological speciesCANDIDA ALBICANS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSeiradake, E. / Mao, W. / Hernandez, V. / Baker, S.J. / Plattner, J.J. / Alley, M.R.K. / Cusack, S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structures of the Human and Fungal Cytosolic Leucyl-tRNA Synthetase Editing Domains: A Structural Basis for the Rational Design of Antifungal Benzoxaboroles.
Authors: Seiradake, E. / Mao, W. / Hernandez, V. / Baker, S.J. / Plattner, J.J. / Alley, M.R.K. / Cusack, S.
History
DepositionApr 4, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOSOLIC LEUCYL-TRNA SYNTHETASE
B: CYTOSOLIC LEUCYL-TRNA SYNTHETASE
C: CYTOSOLIC LEUCYL-TRNA SYNTHETASE
D: CYTOSOLIC LEUCYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)117,9864
Polymers117,9864
Non-polymers00
Water0
1
A: CYTOSOLIC LEUCYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)29,4971
Polymers29,4971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOSOLIC LEUCYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)29,4971
Polymers29,4971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: CYTOSOLIC LEUCYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)29,4971
Polymers29,4971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: CYTOSOLIC LEUCYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)29,4971
Polymers29,4971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.060, 43.040, 122.170
Angle α, β, γ (deg.)90.00, 107.57, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A280 - 302
2111B280 - 302
3111C280 - 302
4111D280 - 302
1211A312 - 339
2211B312 - 339
3211C312 - 339
4211D312 - 339
1311A371 - 383
2311B371 - 383
3311C371 - 383
4311D371 - 383
1411A408 - 465
2411B408 - 465
3411C408 - 465
4411D408 - 465
1511A481 - 527
2511B481 - 527
3511C481 - 527
4511D481 - 527

NCS oper:
IDCodeMatrixVector
1given(-0.999985, 0.002307, -0.00504), (0.002382, 0.999888, -0.014812), (0.005005, -0.014824, -0.999878)-103.8539, -22.0616, -93.9137
2given(0.311512, 0.948227, -0.061849), (-0.936314, 0.295192, -0.190205), (-0.162101, 0.117162, 0.979794)-18.7625, -79.0488, -36.548
3given(0.267172, -0.02164, 0.963405), (-0.014656, 0.999541, 0.026516), (-0.963537, -0.021204, 0.266733)7.4693, 5.8705, -134.4839

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Components

#1: Protein
CYTOSOLIC LEUCYL-TRNA SYNTHETASE


Mass: 29496.615 Da / Num. of mol.: 4 / Fragment: EDITING OR CP1 DOMAIN RESIDUES 280-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH10B / Variant (production host): 10G / References: UniProt: Q5A9A4

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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: 2.3 Å3/Da / Density % sol: 43.5 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM ACETATE, 0.01 M MAGNESIUM ACETATE TETRAHYDRATE, 0.05 M SODIUM CACODYLATE TRIHYDRATE PH 6.5, 30% W/V POLYETHYLENE GLYCOL 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 21666 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.55
Reflection shellResolution: 2.9→3.02 Å / Redundancy: 1.77 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.92 / % possible all: 71.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→28.83 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.816 / SU B: 53.053 / SU ML: 0.454 / Cross valid method: THROUGHOUT / ESU R Free: 0.555 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30085 1112 5.1 %RANDOM
Rwork0.24148 ---
obs0.24457 20555 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.24 Å2
2---0.1 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.9→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7760 0 0 0 7760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227917
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.97810713
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1535976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.24325.286350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.43151406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4351527
X-RAY DIFFRACTIONr_chiral_restr0.0680.21196
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215928
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3251.54886
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.63127921
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.81533031
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4524.52792
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1324 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
3Ctight positional0.020.05
4Dtight positional0.020.05
1Atight thermal2.0630
2Btight thermal1.730
3Ctight thermal2.7630
4Dtight thermal2.0430
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 52 -
Rwork0.292 1048 -
obs--66.83 %
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)
12.13821.7463-0.6092.7142-0.75663.51930.1154-0.1908-0.02530.2333-0.1094-0.2303-0.1128-0.0009-0.0060.05260.0172-0.04140.0348-0.01750.0463-38.697-10.966-35.943
21.5298-0.6475-0.4512.59390.85074.1130.14890.07930.029-0.0704-0.13290.1996-0.0108-0.3564-0.0160.0323-0.021-0.01910.07510.02890.0454-65.07410.308-57.949
31.2794-0.54210.24013.8981-2.14365.01540.0845-0.21060.13620.377-0.02980.0429-0.07030.1569-0.05470.1176-0.0523-0.02170.2053-0.03620.0514-69.7881.23-12.105
43.1091.01660.36323.49480.79911.96610.0959-0.20610.16320.2832-0.0648-0.0150.1084-0.0918-0.03110.2013-0.0246-0.04720.20760.0270.0602-107.352-17.859-18.794
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A279 - 528
2X-RAY DIFFRACTION2B279 - 528
3X-RAY DIFFRACTION3C279 - 529
4X-RAY DIFFRACTION4D279 - 529

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