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- PDB-4ffp: PylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with... -

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Basic information

Entry
Database: PDB / ID: 4ffp
TitlePylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with L-lysine and D-ornithine)
ComponentsPutative uncharacterized protein
KeywordsLIGASE/PRODUCT / amino acid / biosynthesis of pyrrolysine / isopeptide bond formation / ATP-grasp fold / Ligase / ATP-binding / L-lysine and 3R-methyl-D-ornithine / Cytosol / LIGASE-PRODUCT complex
Function / homology
Function and homology information


3-methyl-D-ornithine-L-lysine ligase / pyrrolysine biosynthetic process / ligase activity / amino acid biosynthetic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Pyrrolysine biosynthesis protein PylC / : / PylC-like, N-terminal domain / ATP-grasp fold, PylC-type / ATP-grasp domain / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / NAD(P)-binding Rossmann-like Domain ...Pyrrolysine biosynthesis protein PylC / : / PylC-like, N-terminal domain / ATP-grasp fold, PylC-type / ATP-grasp domain / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N~6~-D-ornithyl-L-lysine / ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / 3-methyl-D-ornithine--L-lysine ligase
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsQuitterer, F. / List, A. / Beck, P. / Bacher, A. / Groll, M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.
Authors: Quitterer, F. / List, A. / Beck, P. / Bacher, A. / Groll, M.
History
DepositionJun 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _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

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1227
Polymers40,8641
Non-polymers1,2586
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.260, 61.260, 172.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1192-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative uncharacterized protein


Mass: 40864.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina barkeri (archaea) / Strain: Fusaro / Gene: Mbar_A0837 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q46E79

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Non-polymers , 5 types, 223 molecules

#2: Chemical ChemComp-0TF / N~6~-D-ornithyl-L-lysine


Mass: 260.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24N4O3
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 1.98 Å3/Da / Density % sol: 37.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES; 200mM MgCl2, 25% PEG4000 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 23067 / Num. obs: 22860 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.8
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 4.1 / % possible all: 97

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 6.966 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18114 1143 5 %RANDOM
Rwork0.15094 ---
all0.154 21716 --
obs0.15245 21716 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.777 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20 Å2
2--1.41 Å20 Å2
3----2.83 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 79 217 3087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022933
X-RAY DIFFRACTIONr_angle_refined_deg2.0542.0183973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0685350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08924.435124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25315505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2891513
X-RAY DIFFRACTIONr_chiral_restr0.1190.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212162
X-RAY DIFFRACTIONr_rigid_bond_restr2.88732932
X-RAY DIFFRACTIONr_sphericity_free24.983559
X-RAY DIFFRACTIONr_sphericity_bonded6.70853042
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 72 -
Rwork0.203 1292 -
obs--94.66 %
Refinement TLS params.Method: refined / Origin x: 14.808 Å / Origin y: 4.984 Å / Origin z: 26.103 Å
111213212223313233
T0.0066 Å20.0022 Å2-0.0045 Å2-0.0039 Å2-0.0002 Å2--0.0049 Å2
L0.1929 °20.0504 °2-0.0131 °2-0.1005 °2-0.0072 °2--0.1947 °2
S0.0003 Å °0.0042 Å °-0.0012 Å °-0.0018 Å °0.0088 Å °0.0123 Å °0.0155 Å °0.0237 Å °-0.0091 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 363
2X-RAY DIFFRACTION1A901 - 906

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