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- PDB-4q3e: PylD cocrystallized with L-Ornithine-Nd-D-lysine and NAD+ -

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Basic information

Entry
Database: PDB / ID: 4q3e
TitlePylD cocrystallized with L-Ornithine-Nd-D-lysine and NAD+
ComponentsPYLD, pyrrolysine synthase
KeywordsOXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / Pyrrolysine
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor / amino acid biosynthetic process / oxidoreductase activity
Similarity search - Function
Rossmann fold - #12150 / Pyrrolysine biosynthesis protein PylD / : / Pyrrolysine biosynthesis protein PylD, N-terminal domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N~5~-D-lysyl-L-ornithine / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Pyrrolysine synthase
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsQuitterer, F. / Beck, P. / Bacher, A. / Groll, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD).
Authors: Quitterer, F. / Beck, P. / Bacher, A. / Groll, M.
History
DepositionApr 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Sep 20, 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 / struct_ref_seq_dif / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYLD, pyrrolysine synthase
B: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,24415
Polymers55,9282
Non-polymers2,31613
Water3,459192
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A: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1558
Polymers27,9641
Non-polymers1,1917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0897
Polymers27,9641
Non-polymers1,1256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: PYLD, pyrrolysine synthase
hetero molecules

B: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,24415
Polymers55,9282
Non-polymers2,31613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_444-x-1/2,-y-1/2,z-1/21
Buried area5740 Å2
ΔGint-84 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.080, 210.460, 77.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1010-

HOH

21A-1062-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.411165, -0.01073, 0.911498), (-0.00684, 0.999939, 0.008685), (-0.911535, -0.002664, -0.411213)-69.53169, 25.79231, 6.73589
Detailstwo molecules in the AU

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PYLD, pyrrolysine synthase


Mass: 27963.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina barkeri (archaea) / Strain: Fusaro / Gene: Mbar_A0835 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q46E80, Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 8 types, 205 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-2YJ / N~5~-D-lysyl-L-ornithine


Type: L-peptide linking / Mass: 260.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24N4O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS; 27% PEG3350; 0.2 M NaCl, pH 8.5, 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: Sep 7, 2013
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: 2.2→20 Å / Num. all: 33346 / Num. obs: 33310 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.8
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4Q39

4q39


Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.211 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21488 1666 5 %RANDOM
Rwork0.17818 ---
obs0.18001 31643 99.89 %-
all-33309 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.372 Å2
Baniso -1Baniso -2Baniso -3
1-5.95 Å2-0 Å2-0 Å2
2---4.04 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 0 151 192 4187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194063
X-RAY DIFFRACTIONr_bond_other_d0.0010.023853
X-RAY DIFFRACTIONr_angle_refined_deg1.2212.0175523
X-RAY DIFFRACTIONr_angle_other_deg0.72638903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3535505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52425.776161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19915648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5731510
X-RAY DIFFRACTIONr_chiral_restr0.0650.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214551
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02857
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 119 -
Rwork0.251 2251 -
obs--100 %
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)
10.15160.10380.1481.2399-0.13530.3745-0.00510.05430.00590.11440.02870.077-0.053-0.0574-0.02360.01880.01620.02250.09720.03120.0601-16.885-17.26216.02
20.035-0.1285-0.02981.6021-0.32090.35210.02160.01150.012-0.01110.05460.1087-0.05470.0488-0.07620.0362-0.01110.04040.09360.00740.0664-29.695-43.64743.88
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 259
2X-RAY DIFFRACTION1A901 - 907
3X-RAY DIFFRACTION1A1001 - 1106
4X-RAY DIFFRACTION2B5 - 259
5X-RAY DIFFRACTION2B901 - 906
6X-RAY DIFFRACTION2B1001 - 1086

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