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- PDB-5urb: Crystal Structure of Methionyl-tRNA synthetase (MetRS) from Acine... -

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Basic information

Entry
Database: PDB / ID: 5urb
TitleCrystal Structure of Methionyl-tRNA synthetase (MetRS) from Acinetobacter baumannii with bound L-Methionine
ComponentsMethionine--tRNA ligase
KeywordsLIGASE / SSGCID / MetRS / amino acid tRNA ligase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Methionyl-tRNA synthetase, Zn-domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 ...Methionyl-tRNA synthetase, Zn-domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Rubrerythrin, domain 2 / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Single Sheet / Rossmann-like alpha/beta/alpha sandwich fold / Nucleic acid-binding, OB-fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
METHIONINE / NITRATE ION / Methionine--tRNA ligase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Methionyl-tRNA synthetase (MetRS) from Acinetobacter baumannii with bound L-Methionine
Authors: Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionine--tRNA ligase
B: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,95424
Polymers128,4862
Non-polymers1,46722
Water18,1411007
1
A: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,03913
Polymers64,2431
Non-polymers79612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,91511
Polymers64,2431
Non-polymers67210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.910, 108.410, 78.570
Angle α, β, γ (deg.)90.000, 90.690, 90.000
Int Tables number4
Space group name H-MP1211
DetailsMonomer as determined by size exclusion chromatography

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methionine--tRNA ligase / Methionyl-tRNA synthetase / MetRS


Mass: 64243.102 Da / Num. of mol.: 2 / Fragment: residues 1-546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: metG, ABUW_3148 / Plasmid: AcbaB.10201.a.A2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D5YKJ7, methionine-tRNA ligase

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Non-polymers , 6 types, 1029 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: NO3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1007 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: AcbaB.10201.a.A2.PW37928 at 40 mg/ml incubated with 5 mM L-Met then mixed 1:1 with an equal volume JCSG+(c3): 20% (w/v) PEG-3350, 200 mM ammonium nitrate, cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2016 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→37.726 Å / Num. obs: 91493 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.799 % / Biso Wilson estimate: 22.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.075 / Χ2: 1.008 / Net I/σ(I): 13.93 / Num. measured all: 347616 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.953.8040.453.1167120.850.52498.9
1.95-23.8290.3683.7265650.8880.42899.3
2-2.063.8250.2884.7264030.9340.33599.3
2.06-2.123.80.2236.0462560.9580.2699.4
2.12-2.193.8290.1847.2759870.9690.21499.3
2.19-2.273.7880.1548.5658120.9780.17999
2.27-2.363.8240.12910.0256100.9840.1599.3
2.36-2.453.8160.11111.2854170.9880.12999.3
2.45-2.563.810.08913.3651830.9920.10499.4
2.56-2.693.7830.07715.4949900.9930.0999.3
2.69-2.833.8080.06717.3247120.9940.07899.5
2.83-33.7960.05819.4644950.9960.06899.4
3-3.213.8080.05121.9442090.9960.05999.4
3.21-3.473.7770.04524.7539080.9970.05299.5
3.47-3.83.7790.0427.3936260.9970.04699.5
3.8-4.253.7630.03629.0632710.9980.04199.6
4.25-4.913.7810.03430.5529110.9970.0499.5
4.91-6.013.7750.03429.6224540.9980.0499.6
6.01-8.53.730.03529.8119150.9970.0499.8
8.5-37.7263.5780.0331.2710570.9980.03697.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(dev_2666)refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RQG

1rqg


Resolution: 1.9→37.726 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.05
RfactorNum. reflection% reflection
Rfree0.1944 2061 2.25 %
Rwork0.1561 --
obs0.157 91459 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.24 Å2 / Biso mean: 28.1013 Å2 / Biso min: 9.89 Å2
Refinement stepCycle: final / Resolution: 1.9→37.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8603 0 86 1012 9701
Biso mean--50.93 37.14 -
Num. residues----1092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069098
X-RAY DIFFRACTIONf_angle_d0.7512390
X-RAY DIFFRACTIONf_chiral_restr0.0481335
X-RAY DIFFRACTIONf_plane_restr0.0041644
X-RAY DIFFRACTIONf_dihedral_angle_d12.865456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.94420.27091420.21685926606899
1.9442-1.99290.25511240.20345931605599
1.9929-2.04670.2781150.19665969608499
2.0467-2.1070.25811360.18525903603999
2.107-2.1750.22681410.17335957609899
2.175-2.25270.23031330.16785919605299
2.2527-2.34290.18411570.16675930608799
2.3429-2.44950.22151430.1665921606499
2.4495-2.57860.2021540.16315953610799
2.5786-2.74010.22071460.16185943608999
2.7401-2.95160.23911260.1659736099100
2.9516-3.24850.19851670.165941610899
3.2485-3.71820.17621250.14376015614099
3.7182-4.68310.13161160.121460276143100
4.6831-37.73390.15361360.1436090622699
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)
10.49120.42140.22921.69360.92531.63420.0613-0.0252-0.12340.25860.1313-0.2850.21020.2394-0.10710.12520.0313-0.03510.1347-0.0040.1558-3.06412.5472-21.9933
21.6042-1.1957-0.26920.3598-0.07290.7207-0.00480.19010.0946-0.0244-0.0361-0.191-0.04720.15550.04580.2004-0.0427-0.01360.19860.0010.1915-0.15143.6938-43.3264
30.85170.65060.6381.81670.81171.43420.01740.0613-0.05850.00540.1453-0.22850.01650.199-0.09740.09530.01720.00970.1437-0.03010.1274-3.414318.7856-26.0648
41.20010.61760.20662.55221.3371.2732-0.04290.0158-0.06620.01950.1725-0.21810.01680.1485-0.09320.1199-0.00710.00490.15550.00140.12014.45843.3691-9.5197
53.5262-1.1070.97734.9543-4.40273.9132-0.3442-0.92261.2601-0.10.2352-0.77920.0540.47180.10440.23730.0232-0.05180.2589-0.00030.25830.043212.2367-29.7952
60.9325-0.0028-0.28853.0475-0.72012.17640.0107-0.0440.10150.2210.22970.4381-0.2852-0.5182-0.08460.15990.07040.06520.20010.02920.1717-34.306439.4026-59.9052
70.7075-0.63530.16790.4241-0.07820.7458-0.01650.1239-0.04160.0033-0.02990.12490.046-0.16750.04310.1754-0.0260.0230.1655-0.02240.1753-31.24649.8273-79.162
80.73150.6323-0.52831.7704-0.9871.3570.00360.0740.0665-0.00890.20660.28860.0453-0.2919-0.13950.12230.0089-0.00230.17380.04380.1523-33.188932.5861-64.6927
91.02460.7407-0.29892.4643-1.29371.3467-0.0178-0.02460.00760.07290.11470.1422-0.0152-0.1275-0.07690.1112-0.01540.00410.16290.00030.101-37.50439.1276-46.6081
103.53893.67463.49975.45335.3749.7864-0.170.044-0.76470.00190.01440.5988-0.1124-0.3440.07820.23230.08950.05650.33090.04710.2467-33.924441.9701-69.045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 113 )A1 - 113
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 249 )A114 - 249
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 360 )A250 - 360
4X-RAY DIFFRACTION4chain 'A' and (resid 361 through 546 )A361 - 546
5X-RAY DIFFRACTION5chain 'A' and (resid 601 through 601 )A601
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 84 )B1 - 84
7X-RAY DIFFRACTION7chain 'B' and (resid 85 through 249 )B85 - 249
8X-RAY DIFFRACTION8chain 'B' and (resid 250 through 386 )B250 - 386
9X-RAY DIFFRACTION9chain 'B' and (resid 387 through 546 )B387 - 546
10X-RAY DIFFRACTION10chain 'B' and (resid 601 through 601 )B601

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