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- PDB-4ffn: PylC in complex with D-ornithine and AMPPNP -

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Basic information

Entry
Database: PDB / ID: 4ffn
TitlePylC in complex with D-ornithine and AMPPNP
ComponentsPylC
KeywordsLIGASE/SUBSTRATE / amino acid / biosynthesis of pyrrolysine / isopeptide bond formation / ATP-grasp fold / Ligase / ATP-binding / L-lysine and 3R-methyl-D-ornithine / Cytosol / LIGASE-SUBSTRATE complex
Function / homology
Function and homology information


3-methyl-D-ornithine-L-lysine ligase / pyrrolysine biosynthetic process / ligase activity / ATP binding / metal ion binding
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ADENOSINE-5'-TRIPHOSPHATE / D-ORNITHINE / 3-methyl-D-ornithine--L-lysine ligase
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: PylC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0586
Polymers40,8641
Non-polymers1,1945
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.150, 60.150, 172.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PylC


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, 205 molecules

#2: Chemical ChemComp-ORD / D-ORNITHINE


Type: D-peptide linking / Mass: 132.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O2
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 1.91 Å3/Da / Density % sol: 35.58 %
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: 2.4→30 Å / Num. all: 13118 / Num. obs: 12371 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.2
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 3.6 / % possible all: 96.4

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.914 / SU B: 14.816 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24933 619 5 %RANDOM
Rwork0.1885 ---
all0.19 11752 --
obs0.1915 11752 94.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.918 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å20 Å20 Å2
2--2.16 Å20 Å2
3----4.31 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 73 200 3064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022946
X-RAY DIFFRACTIONr_angle_refined_deg1.7352.0173970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1575350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05424.435124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71215505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5661513
X-RAY DIFFRACTIONr_chiral_restr0.0970.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212162
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 36 -
Rwork0.223 724 -
obs--96.08 %
Refinement TLS params.Method: refined / Origin x: 14.808 Å / Origin y: 4.984 Å / Origin z: 26.103 Å
111213212223313233
T0.0483 Å2-0.0013 Å2-0.0059 Å2-0.0034 Å20.0083 Å2--0.0333 Å2
L0.269 °20.016 °2-0.0832 °2-0.1409 °2-0.0496 °2--0.1814 °2
S0.0011 Å °0.0053 Å °0.0046 Å °-0.0021 Å °0.014 Å °0.0068 Å °0.006 Å °-0.0029 Å °-0.0151 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 363
2X-RAY DIFFRACTION1A901 - 905

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