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- PDB-3hri: Histidyl-tRNA synthetase (apo) from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 3hri
TitleHistidyl-tRNA synthetase (apo) from Trypanosoma brucei
ComponentsHistidyl-tRNA synthetase
KeywordsLIGASE / apo tRNA-ligase / Aminoacyl-tRNA synthetase / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
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. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histidine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsArakaki, T.L. / Merritt, E.A. / Larson, E.T. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structures of trypanosomal histidyl-tRNA synthetase illuminate differences between eukaryotic and prokaryotic homologs.
Authors: Merritt, E.A. / Arakaki, T.L. / Gillespie, J.R. / Larson, E.T. / Kelley, A. / Mueller, N. / Napuli, A.J. / Kim, J. / Zhang, L. / Verlinde, C.L. / Fan, E. / Zucker, F. / Buckner, F.S. / van ...Authors: Merritt, E.A. / Arakaki, T.L. / Gillespie, J.R. / Larson, E.T. / Kelley, A. / Mueller, N. / Napuli, A.J. / Kim, J. / Zhang, L. / Verlinde, C.L. / Fan, E. / Zucker, F. / Buckner, F.S. / van Voorhis, W.C. / Hol, W.G.
History
DepositionJun 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidyl-tRNA synthetase
B: Histidyl-tRNA synthetase
C: Histidyl-tRNA synthetase
D: Histidyl-tRNA synthetase
E: Histidyl-tRNA synthetase
F: Histidyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)307,2466
Polymers307,2466
Non-polymers00
Water00
1
A: Histidyl-tRNA synthetase
B: Histidyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)102,4152
Polymers102,4152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-29 kcal/mol
Surface area34380 Å2
MethodPISA
2
C: Histidyl-tRNA synthetase
D: Histidyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)102,4152
Polymers102,4152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-32 kcal/mol
Surface area34490 Å2
MethodPISA
3
E: Histidyl-tRNA synthetase
F: Histidyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)102,4152
Polymers102,4152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-28 kcal/mol
Surface area33270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.610, 98.380, 251.969
Angle α, β, γ (deg.)90.000, 90.330, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A44 - 477
2115B44 - 477
3115C44 - 477
4115D44 - 477
5115E44 - 477
6115F44 - 477

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Components

#1: Protein
Histidyl-tRNA synthetase


Mass: 51207.621 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: uncleaved / Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb927.6.2060 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q584V0, histidine-tRNA ligase

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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: 3 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 2 M Lithium Sulfate, 0.1 M HEPES pH 7.3, 1mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97923 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.7→128.322 Å / Num. obs: 99984 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 61 Å2 / Rsym value: 0.166 / Net I/σ(I): 6

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T. cruzi Histidyl-tRNA synthetase

Resolution: 2.85→35 Å / Cor.coef. Fo:Fc: 0.844 / Cor.coef. Fo:Fc free: 0.801 / WRfactor Rfree: 0.318 / WRfactor Rwork: 0.275 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.781 / SU B: 46.029 / SU ML: 0.406 / SU R Cruickshank DPI: 0.649 / SU Rfree: 0.429 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.649 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.313 4225 5 %RANDOM
Rwork0.272 ---
obs0.274 85073 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 20 Å2 / Biso mean: 20 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-0.72 Å2
2---2.25 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.85→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18069 0 0 0 18069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02218449
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212226
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9625073
X-RAY DIFFRACTIONr_angle_other_deg0.875329665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02352347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11523.071788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.193152888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.04915144
X-RAY DIFFRACTIONr_chiral_restr0.0640.22911
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02120649
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023913
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A2179MEDIUM POSITIONAL0.160.25
B2179MEDIUM POSITIONAL0.160.25
C2179MEDIUM POSITIONAL0.170.25
D2179MEDIUM POSITIONAL0.160.25
E2179MEDIUM POSITIONAL0.160.25
E2179MEDIUM POSITIONAL0.170.25
A2621LOOSE POSITIONAL0.225
B2621LOOSE POSITIONAL0.215
C2621LOOSE POSITIONAL0.215
D2621LOOSE POSITIONAL0.245
E2621LOOSE POSITIONAL0.235
F2621LOOSE POSITIONAL0.225
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 289 -
Rwork0.384 5951 -
all-6240 -
obs--99.9 %
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)
11.7964-0.9218-0.5612.92012.15622.2378-0.2815-0.09260.13210.02230.1655-0.07390.28650.38530.1160.3130.05970.09980.15160.08820.2922-32.289-15.5489.107
28.881-4.0309-7.0628-0.86883.388814.89460.14071.78622.2389-0.41670.0257-0.518-0.36150.6705-0.16640.53930.0739-0.16050.79450.31041.0028-39.556-6.117-10.618
31.6466-2.94950.26348.53743.96836.06930.1060.51080.495-0.2112-0.3928-0.5213-0.35160.5180.28690.38290.05690.00750.20170.18880.3328-38.661-7.4672.625
41.2166-0.7492-0.60195.1111-1.48331.7825-0.07510.04130.3703-0.0359-0.0070.0623-0.1589-0.2090.08210.29540.0324-0.03280.0635-0.06360.4342-34.7727.13814.322
55.64392.757-4.46763.8609-3.08514.8942-0.39660.6313-0.06-0.2731-0.1677-0.08170.12690.24480.56440.8082-0.0961-0.10410.64050.23220.655-28.31822.0860.267
64.20740.2878-0.2519.5701-7.67025.2594-0.3979-0.08670.887-0.43320.0006-0.4360.4718-0.08190.39730.3707-0.1122-0.02870.0902-0.06610.6626-33.56613.12315.336
70.9697-0.30870.02334.3977-0.8140.27540.19010.042-0.02710.0638-0.2746-0.08040.02530.19690.08450.34930.01960.02440.2327-0.02630.2559-30.695-17.89716.947
810.82426.3607-3.243114.0361-4.33477.554-0.0294-0.79750.36640.6921-0.1745-0.3336-0.12660.27040.20390.54940.1722-0.21360.2874-0.0030.5161-23.624-42.6732.655
95.1791-2.6172-0.23743.3262-2.4743.3743-0.0607-0.04090.10410.0070.19350.1812-0.047-0.306-0.13280.2458-0.0205-0.02960.0867-0.09910.2943-41.872-21.1928.65
105.0385-11.90640.766323.4182-3.07496.5481-0.26050.2616-0.5452-0.4914-0.45190.075-0.5795-0.40180.71230.7947-0.0319-0.01180.5497-0.17570.6491-34.404-27.988-12.07
110.6043-2.2339-0.02048.4208-0.47267.1670.28550.4849-0.1391-0.9668-0.38040.67770.8262-0.57990.09490.4678-0.01060.03730.4652-0.05870.2565-35.425-28.4011.331
123.65980.9638-0.23596.22291.36810.56510.24480.097-0.3946-0.1866-0.1689-0.00260.00550.0229-0.07590.29720.0733-0.0430.13510.04560.3411-39.401-44.62510.988
132.52761.11594.47872.21641.560315.5061-0.34140.8320.3369-0.8915-0.21870.4696-0.0184-0.75450.56010.71670.0277-0.17450.878-0.11040.9829-45.565-56.969-4.933
146.03912.0284-0.93277.76037.789711.85540.06910.3775-0.54060.29820.07660.10650.1766-0.0265-0.14580.4461-0.00730.03570.0465-0.00710.4631-41.344-49.28311.502
150.686-0.41030.03013.35620.88820.88760.0823-0.04960.0854-0.1015-0.16550.1235-0.0307-0.16730.08320.2975-0.02680.0570.1487-0.0260.3259-43.535-19.87616.714
1611.03365.1285-0.242413.2626-3.64861.235-0.1135-0.897-0.07091.07770.2430.2677-0.1055-0.3361-0.12950.8070.10380.21350.4819-0.0820.4979-50.8342.64235.419
171.6901-0.7339-0.82592.4980.34052.468-0.1389-0.2021-0.28220.1150.1585-0.2416-0.10290.2415-0.01960.3531-0.07880.01760.14210.03120.283611.473-32.1740.544
1811.99355.2040.555918.4781-2.6423-1.2211-0.87380.0233-0.0397-0.96280.7837-1.61-0.45910.14150.09010.9886-0.16810.27090.686-0.11320.658825.288-22.82624.651
197.3347-3.2902-3.50358.98880.28951.63160.3328-0.37070.55960.1903-0.173-0.9087-0.30330.3336-0.15980.5829-0.16390.09340.2260.0540.249714.119-24.131.842
200.510.2451-0.22063.18090.3064-0.11020.01430.15680.2756-0.45990.0086-0.1503-0.0723-0.0067-0.02280.6139-0.01650.00190.15790.07320.36025.88-9.44340.917
2110.37612.52221.3094.73641.13731.53790.34120.27950.1732-0.2576-0.1311-1.021-0.61350.2967-0.21010.5733-0.085-0.00140.42850.1420.986721.3935.54739.832
226.2993.9013-2.2654.0736-1.50515.7003-0.04940.1624-0.2017-0.1587-0.1062-0.1123-0.42220.3690.15560.64690.017-0.00980.1513-0.00840.37215.633-3.45842.463
230.87440.6525-0.25413.4909-0.71941.1149-0.0033-0.1141-0.0038-0.1316-0.1004-0.09940.10060.13670.10360.4194-0.00610.02040.23030.03170.32895.373-34.47945.741
245.11612.81811.10497.81475.386114.3867-0.3145-0.61080.5590.805-0.18020.70060.1434-0.45420.49470.83520.06410.1250.3160.21710.4786-5.123-59.18759.527
252.90070.81330.08381.8662-1.30633.67340.07230.4554-0.1635-0.12070.0480.0233-0.183-0.1562-0.12030.4591-0.03590.04370.13-0.03620.19057.03-37.81331.849
2618.5071-12.4446-0.743214.507-10.18677.30580.66921.2488-1.4284-0.6136-1.6234-0.95110.01680.89580.95420.88490.21490.25690.74210.07751.104128.669-44.78328.059
276.4247-1.5264-1.64777.5899-1.80042.3330.23170.8573-0.45-0.9115-0.4694-0.28340.65320.3970.23780.61230.10180.05420.368-0.09090.360216.609-45.05533.786
280.76030.86420.60881.37860.38122.35960.15110.2046-0.19920.18170.0035-0.22990.85640.1231-0.15460.6890.01420.00440.19220.00250.34986.144-60.96835.165
292.9869-0.2348-6.3653-1.63181.712613.21380.351.2419-0.52570.42720.3007-0.49930.1907-0.0236-0.65071.34220.36370.05440.8665-0.39461.44117.269-73.50820.93
3012.1957-4.10250.70953.90462.4846.12230.0956-0.11350.1879-0.24750.1351-0.19860.86790.1607-0.23070.7238-0.04260.04340.0397-0.00890.42575.235-66.77834.115
310.9139-0.50690.14843.97470.38161.4590.07850.13680.0299-0.2715-0.1921-0.06110-0.18310.11360.3466-0.05790.01850.18220.00350.2232-0.781-36.43834.401
327.25623.59581.89124.62796.726110.81110.17960.1361-0.06690.2807-0.2520.27860.2632-0.67570.07240.61950.1465-0.06440.4580.11110.7702-20.467-13.76237.342
334.5351-2.48720.814.449-2.64393.9813-0.0669-0.36760.26420.16820.4115-0.47890.0911-0.1962-0.34460.34-0.0387-0.02170.1039-0.10450.27566.222-48.30793.948
34-0.23181.5534.527516.8301-6.337813.9641-0.3253-0.039-0.02370.45340.66-1.7411-0.9662-0.0353-0.33470.5302-0.125-0.0920.6667-0.15521.404526.962-38.7897.115
355.2763-0.25751.95317.5734-2.57731.99930.2178-0.47510.72071.3615-0.4053-0.7319-0.81820.23440.18750.7637-0.20640.05620.2332-0.16930.631314.956-40.2191.467
360.09740.25410.03478.16941.10961.2454-0.06830.07380.1811-0.09560.1803-0.6042-0.25560.0412-0.1120.4298-0.039-0.0630.07290.12280.60392.804-25.67189.064
370.28620.07863.54463.29185.476113.4197-0.3620.1842-0.08940.2620.6565-0.2214-0.69111.2175-0.29450.9602-0.1262-0.3540.497-0.14081.525412.103-10.638101.451
383.70666.36770.387313.25041.25150.9819-0.07620.2340.38140.14560.3203-0.3391-0.47290.2345-0.24410.62190.05220.08660.2178-0.05050.68551.264-19.93589.72
390.9159-0.05210.43643.85680.27710.3538-0.0418-0.05760.0484-0.00920.0089-0.17590.0207-0.01260.03290.3557-0.03140.09320.2109-0.00190.267-1.398-50.69291.55
409.07490.8970.39799.29134.321611.734-0.02260.16180.4127-0.0268-0.25230.8755-0.0246-0.99280.27490.3121-0.05460.09750.30640.10980.7867-18.49-75.52790.294
413.93790.502-1.11583.408-0.24383.478-0.13130.4790.1790.1520.2777-0.608-0.10960.1593-0.14650.39150.10830.05040.15060.00840.2811.372-54.03385.749
429.46216.73688.16518.0477-6.242316.59571.04650.8527-0.10970.24650.0598-0.11751.11121.5013-1.10630.73910.2863-0.17250.6628-0.06560.884425.979-60.758102.249
436.19791.2922.61358.0826-1.62661.94820.49830.5412-0.57550.2748-0.4609-1.39440.16990.6834-0.03740.49640.1025-0.1030.3288-0.10550.4114.78-61.15794.994
441.74790.1449-2.01847.31240.0761.49240.0383-0.2464-0.06610.51120.0363-0.5977-0.06210.2108-0.07470.4202-0.0536-0.07150.2295-0.03480.38578.176-77.18886.978
4532.501913.3225-7.477722.563317.659421.5661-0.74845.8429-0.28331.91193.2786-3.0141.6423.3563-2.53020.87790.4595-0.61091.27470.57112.307820.019-89.21387.911
4612.092-1.74412.51647.8796-4.43858.7630.0012-0.3831-0.5362-0.3481-0.0571-0.92640.1510.29520.05590.55560.08140.02690.0797-0.07090.43698.609-83.01585.724
470.8313-0.2958-0.14333.509-0.25020.41560.07460.19260.0411-0.0758-0.0366-0.2839-0.1096-0.0474-0.0380.44540.09260.07760.210.02280.29215.094-52.74580.413
486.1042-4.004-1.574514.15495.13685.5715-0.03310.60980.0831-1.1699-0.05451.2396-0.3482-0.48740.08760.82870.0854-0.06930.57830.17720.3674-7.824-30.29164.949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A47 - 95
2X-RAY DIFFRACTION2A96 - 118
3X-RAY DIFFRACTION3A119 - 170
4X-RAY DIFFRACTION4A171 - 219
5X-RAY DIFFRACTION5A226 - 281
6X-RAY DIFFRACTION6A282 - 318
7X-RAY DIFFRACTION7A319 - 420
8X-RAY DIFFRACTION8A421 - 474
9X-RAY DIFFRACTION9B47 - 95
10X-RAY DIFFRACTION10B96 - 118
11X-RAY DIFFRACTION11B119 - 171
12X-RAY DIFFRACTION12B172 - 219
13X-RAY DIFFRACTION13B226 - 284
14X-RAY DIFFRACTION14B285 - 318
15X-RAY DIFFRACTION15B319 - 420
16X-RAY DIFFRACTION16B421 - 474
17X-RAY DIFFRACTION17C47 - 95
18X-RAY DIFFRACTION18C96 - 118
19X-RAY DIFFRACTION19C119 - 170
20X-RAY DIFFRACTION20C171 - 219
21X-RAY DIFFRACTION21C226 - 281
22X-RAY DIFFRACTION22C282 - 318
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