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- PDB-4q3b: PylD cocrystallized with L-Lysine-Ne-D-lysine and NAD+ -

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Basic information

Entry
Database: PDB / ID: 4q3b
TitlePylD cocrystallized with L-Lysine-Ne-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
Chem-2YF / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Pyrrolysine synthase
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
C: PYLD, pyrrolysine synthase
D: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,80044
Polymers111,8554
Non-polymers5,94440
Water6,269348
1
A: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,73114
Polymers27,9641
Non-polymers1,76713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,98917
Polymers27,9641
Non-polymers2,02516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0567
Polymers27,9641
Non-polymers1,0926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0246
Polymers27,9641
Non-polymers1,0605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: PYLD, pyrrolysine synthase
hetero molecules

B: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,72031
Polymers55,9282
Non-polymers3,79229
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area8780 Å2
ΔGint-67 kcal/mol
Surface area21590 Å2
MethodPISA
6
C: PYLD, pyrrolysine synthase
hetero molecules

D: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,08013
Polymers55,9282
Non-polymers2,15211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area5510 Å2
ΔGint-72 kcal/mol
Surface area20970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.640, 261.170, 48.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-1014-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.983188, 0.182425, 0.00791), (-0.182411, -0.983219, 0.002447), (0.008223, 0.000963, 0.999966)-1.4535, 134.38841, 15.34731
3given(-0.537452, -0.038297, 0.842424), (0.021169, 0.998041, 0.058878), (-0.843028, 0.049478, -0.535589)13.32848, -62.71849, 24.21263
4given(0.527024, 0.180099, 0.830548), (0.115779, -0.983391, 0.139774), (0.841927, 0.022496, -0.539122)-18.97777, 67.75294, 22.28746

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PYLD, pyrrolysine synthase


Mass: 27963.822 Da / Num. of mol.: 4 / Fragment: full length / Mutation: wild type
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, 388 molecules

#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Fragment: full length / Mutation: wild type / Source method: obtained synthetically / Formula: C21H29N7O14P2
References: Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Fragment: full length / Mutation: wild type / Source method: obtained synthetically / Formula: Na
References: Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Fragment: full length / Mutation: wild type / Source method: obtained synthetically / Formula: Mg
References: Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor
#5: Chemical
ChemComp-2YF / N~6~-[(2R)-2,3,4,5-tetrahydropyridin-2-ylcarbonyl]-L-lysine


Type: L-peptide linking / Mass: 255.313 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H21N3O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
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: Oct 26, 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: 1.9→20 Å / Num. all: 89561 / Num. obs: 84511 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.2
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 3.5 / % possible all: 97.6

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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: 1.9→10 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.456 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.157 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22154 4195 5 %RANDOM
Rwork0.1832 ---
obs0.18512 79704 93.78 %-
all-83899 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.002 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.16 Å2-0 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7848 0 391 348 8587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198368
X-RAY DIFFRACTIONr_bond_other_d0.0010.027972
X-RAY DIFFRACTIONr_angle_refined_deg1.4272.02311344
X-RAY DIFFRACTIONr_angle_other_deg0.782318424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65151036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11525.802324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.981151328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.61520
X-RAY DIFFRACTIONr_chiral_restr0.0760.21323
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219304
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021736
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 310 -
Rwork0.259 5883 -
obs--97.91 %
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)
10.61230.18880.04670.2899-0.09440.07260.0248-0.0443-0.0345-0.007-0.0349-0.0750.0095-0.03260.01010.2824-0.0092-0.0040.21550.02440.03831.98951.89223.134
20.64410.0651-0.29020.3013-0.15970.20740.01650.0090.0467-0.00680.05430.0992-0.01290.0135-0.07090.27990.01830.00720.21410.04760.053511.72981.7527.611
31.70570.0035-0.39090.4132-0.08220.2378-0.0304-0.02220.1880.02390.1010.15280.02610.0505-0.07060.25010.046-0.0110.06670.06950.27069.428114.762-2.226
40.69190.36380.52810.72130.06980.5115-0.0225-0.0163-0.20710.00170.0685-0.2289-0.0683-0.0427-0.04590.2288-0.00810.00920.0124-0.02190.31369.92419.39414.739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 259
2X-RAY DIFFRACTION1A901 - 913
3X-RAY DIFFRACTION1A1001 - 1149
4X-RAY DIFFRACTION2B0 - 259
5X-RAY DIFFRACTION2B901 - 916
6X-RAY DIFFRACTION2B1001 - 1134
7X-RAY DIFFRACTION3C0 - 259
8X-RAY DIFFRACTION3C901 - 906
9X-RAY DIFFRACTION3C1001 - 1034
10X-RAY DIFFRACTION4D0 - 259
11X-RAY DIFFRACTION4D901 - 905
12X-RAY DIFFRACTION4D1001 - 1031

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