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- PDB-3gdz: Crystal structure of arginyl-tRNA synthetase from Klebsiella pneu... -

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Basic information

Entry
Database: PDB / ID: 3gdz
TitleCrystal structure of arginyl-tRNA synthetase from Klebsiella pneumoniae subsp. pneumoniae
ComponentsArginyl-tRNA synthetase
KeywordsLIGASE / Arginyl-tRNA synthetase / Klebsiella pneumoniae subsp. pneumoniae MGH 78578 / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Aminoacyl-tRNA synthetase / ATP-binding / Nucleotide-binding / Protein biosynthesis
Function / homology
Function and homology information


arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Arginyl tRNA synthetase N-terminal domain / Arginine-tRNA ligase / Arginyl tRNA synthetase N-terminal domain / Arginyl-tRNA synthetase, catalytic core domain / Arginyl tRNA synthetase N-terminal domain superfamily / tRNA synthetases class I (R) / Arginyl tRNA synthetase N terminal domain / DALR anticodon binding domain / Arginyl tRNA synthetase N terminal dom / DALR anticodon binding ...Arginyl tRNA synthetase N-terminal domain / Arginine-tRNA ligase / Arginyl tRNA synthetase N-terminal domain / Arginyl-tRNA synthetase, catalytic core domain / Arginyl tRNA synthetase N-terminal domain superfamily / tRNA synthetases class I (R) / Arginyl tRNA synthetase N terminal domain / DALR anticodon binding domain / Arginyl tRNA synthetase N terminal dom / DALR anticodon binding / DALR anticodon binding domain / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Gyrase A; domain 2 / Rossmann-like alpha/beta/alpha sandwich fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Arginine--tRNA ligase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsChang, C. / Wu, R. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of arginyl-tRNA synthetase from Klebsiella pneumoniae subsp. pneumoniae
Authors: Chang, C. / Wu, R. / Bearden, J. / Joachimiak, A.
History
DepositionFeb 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginyl-tRNA synthetase
B: Arginyl-tRNA synthetase
C: Arginyl-tRNA synthetase
D: Arginyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,28213
Polymers46,7234
Non-polymers5599
Water3,441191
1
A: Arginyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9295
Polymers11,6811
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arginyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7432
Polymers11,6811
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Arginyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8674
Polymers11,6811
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Arginyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7432
Polymers11,6811
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.351, 41.966, 71.464
Angle α, β, γ (deg.)90.00, 91.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Arginyl-tRNA synthetase / Arginine-tRNA ligase / ArgRS


Mass: 11680.850 Da / Num. of mol.: 4 / Fragment: UNP residues 1-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: MGH 78578 / Gene: argS, KPN78578_23530, KPN_02388 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: A6TB43, arginine-tRNA ligase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 1.4M Sodium citrate tribasic dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Feb 6, 2009
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 21585 / Num. obs: 21569 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 17.5
Reflection shellResolution: 2.2→2.22 Å / Redundancy: 6 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3.11 / Num. unique all: 523 / % possible all: 98.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9 / SU B: 13.402 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.23
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24777 1103 5.1 %RANDOM
Rwork0.19226 ---
all0.19516 21504 --
obs0.19516 21504 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.869 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å2-0.21 Å2
2---1.65 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 36 191 3343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223378
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.974583
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7725460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37726.447152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73615569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2161515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212627
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_it0.6331.52228
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19923551
X-RAY DIFFRACTIONr_scbond_it2.36831150
X-RAY DIFFRACTIONr_scangle_it3.8194.51032
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 81 -
Rwork0.188 1413 -
obs-1494 98.68 %
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)
11.4511-0.11651.54351.56132.92988.67930.07090.0628-0.0805-0.0207-0.0091-0.0792-0.08570.1195-0.06180.0227-0.0049-0.02620.00640.00790.046181.553129.684350.6189
21.6751-0.13470.90921.8558-0.30753.28130.1277-0.1504-0.07880.22420.01990.05130.2152-0.1569-0.14760.0523-0.0153-0.01320.01550.01030.035375.159325.204456.5672
39.1558-0.5526-1.59372.45161.80727.8590.05240.27090.4053-0.35820.14520.0439-0.27340.0249-0.19760.0593-0.0199-0.01210.01980.01620.02873.426629.961732.64
46.09521.40363.881.51251.77945.1163-0.15090.167-0.0622-0.03430.2079-0.1911-0.19230.0947-0.0570.05260.00440.0080.0417-0.02630.05352.340329.968475.2969
52.4035-0.38230.51532.2768-0.50931.6514-0.0231-0.1509-0.09820.14890.0704-0.1043-0.0011-0.0917-0.04730.02070.0021-0.00260.01230.00470.01550.995924.662883.7884
61.0080.91051.57681.7071-0.05699.74930.0364-0.06070.0297-0.06560.0031-0.081-0.154-0.1407-0.03950.042-0.01140.03170.0085-0.0130.032534.816229.65665.7795
77.66373.8135-6.77661.9422-3.178.2136-0.0180.10530.0802-0.04840.04130.03780.0428-0.1948-0.02330.06160.00750.00570.0112-0.01440.056238.199619.498852.3851
81.8389-0.1733-0.58261.99010.17473.3310.0082-0.0575-0.0065-0.06490.0301-0.1460.12950.1757-0.03830.00870.00580.00630.0099-0.00260.024546.436214.396953.6283
99.060.4556-1.88391.03080.6732.5149-0.1724-0.14380.09380.09350.0081-0.0220.1119-0.04840.16430.02250.0051-0.00220.0078-0.01360.029429.170719.335870.6187
1010.1046-2.8826-1.20362.17070.58990.2159-0.1924-0.16220.21630.06180.1591-0.0410.03280.03980.03330.038-0.00150.00790.012200.099954.615640.021447.9936
113.05570.1093-1.54261.9438-0.42451.8415-0.04680.2241-0.0774-0.00930.01930.18830.1328-0.0980.02760.0246-0.00420.00510.0174-0.00460.021748.482135.603241.7502
128.61870.4576.54953.19282.40047.0757-0.11430.59860.01850.20270.1409-0.149-0.03510.4808-0.02650.0440.01430.0120.05330.00790.051171.439540.184238.523
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 19
2X-RAY DIFFRACTION2A20 - 88
3X-RAY DIFFRACTION3A89 - 103
4X-RAY DIFFRACTION4B1 - 19
5X-RAY DIFFRACTION5B20 - 88
6X-RAY DIFFRACTION6B89 - 103
7X-RAY DIFFRACTION7C1 - 19
8X-RAY DIFFRACTION8C20 - 88
9X-RAY DIFFRACTION9C89 - 103
10X-RAY DIFFRACTION10D1 - 19
11X-RAY DIFFRACTION11D20 - 88
12X-RAY DIFFRACTION12D89 - 103

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