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- PDB-8ke4: PylRS C-terminus domain mutant bound with D-3-bromophenylalanine ... -

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Basic information

Entry
Database: PDB / ID: 8ke4
TitlePylRS C-terminus domain mutant bound with D-3-bromophenylalanine and AMPNP
ComponentsPyrrolysine--tRNA ligase
KeywordsLIGASE / tRNA Synthetase
Function / homology
Function and homology information


pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
Pyrrolysyl-tRNA ligase / Pyrrolysyl-tRNA ligase, N-terminal / Pyrrolysyl-tRNA ligase, C-terminal / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / 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)
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / (2R)-2-azanyl-3-(3-bromophenyl)propanoic acid / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75050958755 Å
AuthorsWeng, J.H. / Tsai, M.D. / Wang, Y.S.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-KPQ-109-TPP2 Taiwan
Academia Sinica (Taiwan)AS-KPQ-105-TPP Taiwan
Ministry of Science and Technology (MoST, Taiwan)107-2113-M-001-025-MY3 Taiwan
CitationJournal: Front Genet / Year: 2023
Title: Rational design of the genetic code expansion toolkit for in vivo encoding of D-amino acids.
Authors: Jiang, H.K. / Weng, J.H. / Wang, Y.H. / Tsou, J.C. / Chen, P.J. / Ko, A.A. / Soll, D. / Tsai, M.D. / Wang, Y.S.
History
DepositionAug 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7985
Polymers32,0001
Non-polymers7994
Water4,864270
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,59710
Polymers63,9992
Non-polymers1,5988
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
Buried area7180 Å2
ΔGint-56 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.198, 105.198, 71.694
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

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Components

#1: Protein Pyrrolysine--tRNA ligase / Pyrrolysyl-tRNA synthetase / PylRS


Mass: 31999.602 Da / Num. of mol.: 1 / Fragment: C-terminus domain / Mutation: N346G,C348Q,V401G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: pylS, DU43_20175, DU67_18120 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F8JXW8, pyrrolysine-tRNAPyl ligase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FXF / (2R)-2-azanyl-3-(3-bromophenyl)propanoic acid


Type: D-peptide linking / Mass: 244.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10BrNO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES buffer pH 7.5, 10% PEG 8000, 10% Ethylene Glycerol

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→28.2 Å / Num. obs: 45530 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 24.3372328819 Å2 / Rpim(I) all: 0.017 / Rrim(I) all: 0.056 / Net I/σ(I): 55.5
Reflection shell
Resolution (Å)Num. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID
3.77-28.246410.9990.0120.0391
2.99-3.7745910.9990.0140.0481
2.61-2.9945540.9990.0170.0571
2.37-2.6145630.9980.0210.071
2.2-2.3745440.9970.0250.0851
2.07-2.245420.9970.030.1011
1.97-2.0745580.9950.0390.1331
1.89-1.9744980.9920.0570.1921
1.81-1.8945090.9770.0920.3121
1.75-1.8145300.9620.1320.4451

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZCE

2zce


Resolution: 1.75050958755→28.1702948531 Å / SU ML: 0.151687980204 / Cross valid method: FREE R-VALUE / σ(F): 1.38114917239 / Phase error: 18.3268843451
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.184316416937 2011 4.41939170183 %
Rwork0.172443704989 43493 -
obs0.172967683239 45504 99.9802254301 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.2227081296 Å2
Refinement stepCycle: LAST / Resolution: 1.75050958755→28.1702948531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 46 271 2428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008302885843412201
X-RAY DIFFRACTIONf_angle_d1.118959638722969
X-RAY DIFFRACTIONf_chiral_restr0.0681734680093321
X-RAY DIFFRACTIONf_plane_restr0.00873296646534381
X-RAY DIFFRACTIONf_dihedral_angle_d23.740654366849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75051-1.79430.2528774446251420.2358506256413096X-RAY DIFFRACTION100
1.7943-1.84280.237793828341390.2040498878463098X-RAY DIFFRACTION100
1.8428-1.8970.2281724328531390.1981784969133069X-RAY DIFFRACTION100
1.897-1.95820.2092914070551430.1825319815153124X-RAY DIFFRACTION100
1.9582-2.02820.2143569286131410.1836482756953061X-RAY DIFFRACTION100
2.0282-2.10940.2096939200741470.1863244363563097X-RAY DIFFRACTION100
2.1094-2.20530.2100291168431450.1766217334973091X-RAY DIFFRACTION100
2.2053-2.32150.2155798972221490.1769878601873102X-RAY DIFFRACTION100
2.3215-2.46690.20165792521440.1751506952213111X-RAY DIFFRACTION100
2.4669-2.65730.1876148929361470.1810768879283107X-RAY DIFFRACTION100
2.6573-2.92440.1800386270171420.177008489883116X-RAY DIFFRACTION100
2.9244-3.3470.1836629672181420.1691488774453099X-RAY DIFFRACTION100
3.347-4.21460.165805267281440.1553548337243154X-RAY DIFFRACTION100
4.2146-28.170.1512392208951470.1626966259553168X-RAY DIFFRACTION99.7292418773

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