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- PDB-4rdx: Structure of histidinyl-tRNA synthetase in complex with tRNA(His) -

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Basic information

Entry
Database: PDB / ID: 4rdx
TitleStructure of histidinyl-tRNA synthetase in complex with tRNA(His)
Components
  • Histidine--tRNA ligase
  • tRNA(his)
KeywordsLIGASE/RNA / aminoacyl-tRNA synthetase / classII aaRS / aminoacylation / histidine / tRNA / LIGASE-RNA complex
Function / homology
Function and homology information


histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / HISTIDINE / : / RNA / RNA (> 10) / Histidine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsXie, W. / Tian, Q. / Wang, C.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural basis for recognition of G-1-containing tRNA by histidyl-tRNA synthetase
Authors: Tian, Q. / Wang, C. / Liu, Y. / Xie, W.
History
DepositionSep 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Derived calculations / Structure summary
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine--tRNA ligase
C: tRNA(his)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0954
Polymers72,5922
Non-polymers5032
Water1,36976
1
A: Histidine--tRNA ligase
C: tRNA(his)
hetero molecules

A: Histidine--tRNA ligase
C: tRNA(his)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,1918
Polymers145,1844
Non-polymers1,0074
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area18510 Å2
ΔGint-91 kcal/mol
Surface area53540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.061, 159.703, 123.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Histidine--tRNA ligase / Histidyl-tRNA synthetase / HisRS


Mass: 47264.129 Da / Num. of mol.: 1 / Fragment: histidinyl-tRNA synthetase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: hisS, TT_C0360 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62374, histidine-tRNA ligase
#2: RNA chain tRNA(his)


Mass: 25327.889 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB27 (bacteria) / References: GenBank: 46197919
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 4.5
Details: 5% PEG4000, 0.1M NaOAc pH4.5, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 27434 / Num. obs: 27099 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.6 / Redundancy: 5.4 % / Biso Wilson estimate: 48.73 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 13.9
Reflection shellResolution: 2.55→2.55 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2692 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H4V and 3WC1

1h4v

3wc1


Resolution: 2.55→29.469 Å / SU ML: 0.39 / σ(F): 1.35 / σ(I): 2.6 / Phase error: 33.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 1362 5.04 %5.04% of the reflections
Rwork0.2073 ---
obs0.21 27018 97.86 %-
all-27018 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→29.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3217 1654 34 76 4981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035159
X-RAY DIFFRACTIONf_angle_d0.87349
X-RAY DIFFRACTIONf_dihedral_angle_d17.6152220
X-RAY DIFFRACTIONf_chiral_restr0.048866
X-RAY DIFFRACTIONf_plane_restr0.004667
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.55-2.64020.43731140.345232989
2.6402-2.74580.33691420.3018255999
2.7458-2.87070.32281440.26982574100
2.8707-3.02190.31671330.25312612100
3.0219-3.2110.28781270.2216258699
3.211-3.45860.24891470.19912584100
3.4586-3.8060.23861240.17382618100
3.806-4.35520.22581490.1737258599
4.3552-5.48130.21741360.1788261798
5.4813-29.4710.25831460.2074259294
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)
12.4002-0.4953-0.37472.4031-0.80111.63450.0261-0.05710.1646-0.1898-0.05420.092-0.29520.03280.07070.569-0.0023-0.02570.4183-0.0240.2737.2996158.9661129.3146
25.46-1.16971.16975.0296-1.42244.97360.00870.1872-0.5253-0.1250.44090.95370.0257-0.5118-0.19950.5780.0373-0.01420.4228-0.02080.490119.3135152.4888125.5182
31.7075-0.7291-0.05713.0984-0.20621.52660.0450.0906-0.1073-0.2966-0.12660.13060.08620.01220.10950.4471-0.0011-0.00590.3991-0.01360.267734.9927146.2112131.3197
43.49852.6896-1.42784.7875-1.61592.06180.3375-0.6435-0.14670.151-0.3192-0.2314-0.05720.43070.08670.5829-0.017-0.01010.54230.04060.27342.6018147.2224145.3436
50.6199-0.46241.01887.47520.61882.2513-0.2582-0.1139-0.13470.66710.34471.51120.0602-0.4036-0.01850.5902-0.0330.14540.56940.11780.613416.8417138.0021155.8546
67.01421.3307-4.07577.15431.32077.80830.27780.9740.6975-0.39320.12530.5215-0.4634-0.5573-0.11050.86310.1065-0.06210.72070.08110.669713.5538146.9892152.9698
73.86261.4663-1.39353.4044-0.45773.87490.05560.09990.60860.105-0.2723-0.119-0.3034-0.1301-0.18240.71870.06350.07170.48280.06340.523822.0578147.0966158.3262
83.2620.6007-2.62960.651-0.15192.40360.0727-0.187-0.19790.3069-0.04420.07030.26810.0050.17180.6576-0.00820.00360.37340.04540.35534.9748136.036148.8448
99.00246.4931-2.74482.0052-1.19072.15430.257-1.16130.88950.9255-0.1217-0.1209-0.78520.4221-0.61721.17680.08650.01210.520.01270.313240.1058155.9702149.6839
101.0715-0.5462-0.49851.019-1.00024.15990.0361-0.1415-0.02290.4836-0.1371-0.06860.0380.16030.03820.48410.03910.06040.38360.04720.310437.0869150.962137.7076
116.4162-0.23651.10131.7237-3.04767.23350.1623-0.2365-0.10810.6411-0.123-0.0754-0.26940.0362-0.01230.5483-0.0979-0.0230.4075-0.01740.318353.9885186.0871116.8061
126.78031.4996-0.18026.9103-0.87649.68760.3968-0.5218-0.00860.7283-0.1986-0.8258-0.8470.4207-0.01410.5963-0.1024-0.16790.5531-0.03670.494663.592187.0863118.7687
13-0.12760.05380.0534-0.04190.01920.0086-0.2718-0.00260.72670.8833-0.27010.2157-0.942-0.167100.44420.11160.31440.3368-0.07040.198318.641170.617149.904
140.08620.03810.23050.19420.05110.09990.0514-0.68730.31330.2511-0.09920.09970.2662-0.5347-00.65060.16980.08760.8174-0.06530.622829.7519189.2896147.5049
15-0.024-0.0023-0.04420.0404-0.0279-0.0246-0.2717-0.2801-0.32730.1762-0.1287-0.3854-0.4284-0.499900.5112-0.08270.08080.19480.01820.549624.4151200.9197149.5561
16-0.01940.0023-0.01530.00660.0012-0.0024-0.21180.070.30950.0207-0.063-0.2551-0.11070.184400.8824-0.00610.26280.65030.17311.102142.802193.7463134.5269
170.0012-0.00070.0017-0.00330.00310.0029-0.12670.009-0.01480.0412-0.00940.1892-0.01730.0324-02.22510.1448-0.18912.2082-0.26211.53453.865206.9718128.7582
18-0.00190.0245-0.0338-0.01660.04340.00510.0285-0.4699-0.0196-0.062-0.02140.06310.21930.19101.0018-0.2290.02210.6234-0.06740.601858.3723197.1375131.757
19-0.00810.01650.0013-0.0028-0.00430.00280.0779-0.090.14960.1179-0.0306-0.1623-0.16170.018201.27620.08630.05840.84960.12811.279339.6156202.6903134.9231
200.0052-0.0038-0.0228-0.00270.00510.0085-0.04610.160.1556-0.3676-0.31340.17930.03750.045700.64970.13570.28080.54220.15930.641625.169193.8515137.4113
21-0.0806-0.0543-0.223-0.0030.101-0.1548-0.09150.1754-0.05470.3356-0.88720.67270.14860.233100.56030.13760.37940.2747-0.16850.485811.527190.5592148.4805
22-0.0158-0.01670.11240.0028-0.0533-0.00060.1183-0.04960.00730.1852-0.16380.1747-0.2797-0.2585-00.71020.04510.05680.3445-0.0060.394622.5096163.3578145.0847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:48 )A2 - 48
2X-RAY DIFFRACTION2( CHAIN A AND RESID 49:81 )A49 - 81
3X-RAY DIFFRACTION3( CHAIN A AND RESID 82:147 )A82 - 147
4X-RAY DIFFRACTION4( CHAIN A AND RESID 148:169 )A148 - 169
5X-RAY DIFFRACTION5( CHAIN A AND RESID 170:192 )A170 - 192
6X-RAY DIFFRACTION6( CHAIN A AND RESID 193:200 )A193 - 200
7X-RAY DIFFRACTION7( CHAIN A AND RESID 201:218 )A201 - 218
8X-RAY DIFFRACTION8( CHAIN A AND RESID 219:270 )A219 - 270
9X-RAY DIFFRACTION9( CHAIN A AND RESID 271:275 )A271 - 275
10X-RAY DIFFRACTION10( CHAIN A AND RESID 276:326 )A276 - 326
11X-RAY DIFFRACTION11( CHAIN A AND RESID 327:369 )A327 - 369
12X-RAY DIFFRACTION12( CHAIN A AND RESID 370:421 )A370 - 421
13X-RAY DIFFRACTION13( CHAIN C AND RESID 1:7 )C1 - 7
14X-RAY DIFFRACTION14( CHAIN C AND RESID 8:17 )C8 - 17
15X-RAY DIFFRACTION15( CHAIN C AND RESID 18:23 )C18 - 23
16X-RAY DIFFRACTION16( CHAIN C AND RESID 24:29 )C24 - 29
17X-RAY DIFFRACTION17( CHAIN C AND RESID 30:33 )C30 - 33
18X-RAY DIFFRACTION18( CHAIN C AND RESID 34:40 )C34 - 40
19X-RAY DIFFRACTION19( CHAIN C AND RESID 41:44 )C41 - 44
20X-RAY DIFFRACTION20( CHAIN C AND RESID 45:48 )C45 - 48
21X-RAY DIFFRACTION21( CHAIN C AND RESID 49:65 )C49 - 65
22X-RAY DIFFRACTION22( CHAIN C AND RESID 66:76 )C66 - 76

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