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- PDB-4q3c: PylD cocrystallized with L-Lysine-Ne-L-lysine and NAD+ -

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Basic information

Entry
Database: PDB / ID: 4q3c
TitlePylD cocrystallized with L-Lysine-Ne-L-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~6~-L-lysyl-L-lysine / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Pyrrolysine synthase
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.1Apr 30, 2014Group: Structure summary
Revision 1.2Jul 2, 2014Group: Database references
Revision 1.3Aug 20, 2014Group: Database references
Revision 1.4Sep 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 1.5Oct 30, 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)116,45628
Polymers111,8554
Non-polymers4,60124
Water4,918273
1
A: PylD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,41111
Polymers27,9641
Non-polymers1,44810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PylD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1477
Polymers27,9641
Non-polymers1,1836
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PylD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9495
Polymers27,9641
Non-polymers9854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PylD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9495
Polymers27,9641
Non-polymers9854
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)58,55918
Polymers55,9282
Non-polymers2,63116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area6290 Å2
ΔGint-67 kcal/mol
Surface area21000 Å2
MethodPISA
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C: PylD, pyrrolysine synthase
hetero molecules

D: PylD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,89810
Polymers55,9282
Non-polymers1,9708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area4690 Å2
ΔGint-75 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.250, 259.770, 48.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.986375, 0.164432, 0.005198), (-0.16444, -0.986386, -0.001306), (0.004912, -0.002143, 0.999986)0.90798, 133.52715, 15.91163
3given(-0.544518, -0.034984, 0.838019), (0.028481, 0.997782, 0.06016), (-0.838266, 0.056626, -0.542314)13.58919, -62.36528, 23.3923
4given(0.531105, 0.159981, 0.832066), (0.10026, -0.98698, 0.12577), (0.841353, 0.016626, -0.54023)-17.9229, 67.60268, 22.16523

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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
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, 297 molecules

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


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-2YG / N~6~-L-lysyl-L-lysine


Type: L-peptide linking / Mass: 274.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26N4O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
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: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 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: 2.1→20 Å / Num. all: 66293 / Num. obs: 66181 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 3.1 / % 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: 2.1→15 Å / SU B: 9.944 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19796 3260 4.9 %RANDOM
Rwork0.16899 ---
obs0.17044 62849 99.85 %-
all-66109 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.106 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-0 Å2
2---1.35 Å20 Å2
3---3.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7816 0 295 273 8384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198253
X-RAY DIFFRACTIONr_bond_other_d0.0020.027843
X-RAY DIFFRACTIONr_angle_refined_deg1.512.01611221
X-RAY DIFFRACTIONr_angle_other_deg0.799318113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8751031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35825.802324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.163151321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3121520
X-RAY DIFFRACTIONr_chiral_restr0.0790.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021738
X-RAY DIFFRACTIONr_rigid_bond_restr2.563316092
X-RAY DIFFRACTIONr_sphericity_free37.4745102
X-RAY DIFFRACTIONr_sphericity_bonded26.829516125
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 218 -
Rwork0.253 4493 -
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)
10.01790.0242-0.00940.03790.00220.05310.0018-0.00830.00110.0075-0.00180.00170.00540.020400.06130.0032-00.0867-0.0010.00052.54551.47523.351
20.0031-0.00080.01110.0038-0.01540.0849-0.0017-0.0060.00280.00040.00130.0015-0.0115-0.02840.00040.06190.00020.00230.0868-0.00150.005112.0281.2637.495
30.1746-0.0044-0.0720.18070.0310.12380.01690.00780.0346-0.0031-0.01210.0179-0.0293-0.0228-0.00480.08170.0008-0.0050.1134-0.00090.00989.368113.916-2.423
40.15590.11630.14520.22110.04470.16790.06460.0395-0.03270.0405-0.0401-0.02230.07060.0702-0.02440.0755-0.01940.00450.1363-0.00490.018910.20919.20814.304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 259
2X-RAY DIFFRACTION1A901 - 910
3X-RAY DIFFRACTION1A1001 - 1133
4X-RAY DIFFRACTION2B1 - 259
5X-RAY DIFFRACTION2B901 - 906
6X-RAY DIFFRACTION2B1001 - 1111
7X-RAY DIFFRACTION3C1 - 259
8X-RAY DIFFRACTION3C901 - 904
9X-RAY DIFFRACTION3C1001 - 1016
10X-RAY DIFFRACTION4D2 - 259
11X-RAY DIFFRACTION4D901 - 904
12X-RAY DIFFRACTION4D1001 - 1013

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