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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 / homologyun:q5a9a4:
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.
Validation Report
SummaryFull reportAbout validation report
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

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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
γ
α
β
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:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDAuth asym-IDAuth seq-ID
11A280 - 302
21B280 - 302
31C280 - 302
41D280 - 302
12A312 - 339
22B312 - 339
32C312 - 339
42D312 - 339
13A371 - 383
23B371 - 383
33C371 - 383
43D371 - 383
14A408 - 465
24B408 - 465
34C408 - 465
44D408 - 465
15A481 - 527
25B481 - 527
35C481 - 527
45D481 - 527

NCS oper:

Code: given

IDMatrixVector
1(-0.999985, 0.002307, -0.00504), (0.002382, 0.999888, -0.014812), (0.005005, -0.014824, -0.999878)-103.8539, -22.0616, -93.9137
2(0.311512, 0.948227, -0.061849), (-0.936314, 0.295192, -0.190205), (-0.162101, 0.117162, 0.979794)-18.7625, -79.0488, -36.548
3(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/peptide
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

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0070.0227917
r_bond_other_d
r_angle_refined_deg1.0231.97810713
r_angle_other_deg
r_dihedral_angle_1_deg5.1535976
r_dihedral_angle_2_deg40.24325.286350
r_dihedral_angle_3_deg17.43151406
r_dihedral_angle_4_deg9.4351527
r_chiral_restr0.0680.21196
r_gen_planes_refined0.0040.0215928
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it0.3251.54886
r_mcbond_other
r_mcangle_it0.63127921
r_mcangle_other
r_scbond_it0.81533031
r_scbond_other
r_scangle_it1.4524.52792
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Refine LS restraints NCS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)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

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDAuth asym-IDAuth seq-ID
11A279 - 528
22B279 - 528
33C279 - 529
44D279 - 529

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