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- PDB-4q3a: PylD cocrystallized with L-Lysine-Ne-3S-methyl-L-ornithine and NAD+ -

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Basic information

Entry
Database: PDB / ID: 4q3a
TitlePylD cocrystallized with L-Lysine-Ne-3S-methyl-L-ornithine and NAD+
ComponentsPYLD, pyrrolysine synthase
KeywordsOXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / Pyrrolysine
Function / homology
Function and homology information


nucleotide binding / metal ion binding
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-2YC / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Pyrrolysine biosynthesis protein PylD N-terminal domain-containing protein
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

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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)118,33452
Polymers111,8554
Non-polymers6,47948
Water5,873326
1
A: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,86916
Polymers27,9641
Non-polymers1,90515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,32322
Polymers27,9641
Non-polymers2,35921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2109
Polymers27,9641
Non-polymers1,2468
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9325
Polymers27,9641
Non-polymers9684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: PYLD, pyrrolysine synthase
hetero molecules

A: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,19238
Polymers55,9282
Non-polymers4,26436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area10200 Å2
ΔGint-77 kcal/mol
Surface area21360 Å2
MethodPISA
6
C: PYLD, pyrrolysine synthase
hetero molecules

D: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,14214
Polymers55,9282
Non-polymers2,21412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area5200 Å2
ΔGint-77 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.490, 259.850, 48.660
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(-0.981354, -0.191733, 0.013489), (0.191558, -0.981392, -0.013251), (0.015779, -0.01042, 0.999821)2.07109, 133.90915, -14.0679
3given(-0.538959, 0.035398, 0.841588), (-0.018424, 0.998382, -0.053792), (-0.842131, -0.044497, -0.537435)-13.06004, -62.4713, -24.71851
4given(0.534362, -0.179196, 0.826042), (-0.129217, -0.983101, -0.129677), (0.83532, -0.037444, -0.548487)18.63707, 67.6429, -21.69028

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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 , 9 types, 374 molecules

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


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#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-2YC / N~6~-{[(2S,3S)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine


Type: L-peptide linking / Mass: 255.313 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H21N3O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
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: Nov 10, 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: 2.2→40 Å / Num. all: 57676 / Num. obs: 57408 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.3
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0032refinement
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: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.584 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.247 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20448 2865 5 %RANDOM
Rwork0.16936 ---
obs0.17112 54490 99.58 %-
all-57355 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.118 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0 Å20 Å2
2--0.86 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7826 0 423 326 8575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198371
X-RAY DIFFRACTIONr_bond_other_d0.0010.027983
X-RAY DIFFRACTIONr_angle_refined_deg1.2732.02511342
X-RAY DIFFRACTIONr_angle_other_deg0.748318444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43551033
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52225.789323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.668151323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.841520
X-RAY DIFFRACTIONr_chiral_restr0.0650.21325
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021733
X-RAY DIFFRACTIONr_mcbond_it1.0642.6544152
X-RAY DIFFRACTIONr_mcbond_other1.0642.6534149
X-RAY DIFFRACTIONr_mcangle_it1.8373.9755177
X-RAY DIFFRACTIONr_mcangle_other1.8373.9755177
X-RAY DIFFRACTIONr_scbond_it1.352.9074219
X-RAY DIFFRACTIONr_scbond_other1.352.9074219
X-RAY DIFFRACTIONr_scangle_other2.0664.2416166
X-RAY DIFFRACTIONr_long_range_B_refined5.64621.7579303
X-RAY DIFFRACTIONr_long_range_B_other5.52721.5879218
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 205 -
Rwork0.21 3889 -
obs--99.83 %
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)
10.6918-0.21140.07660.35140.12490.14730.05610.0464-0.0156-0.0165-0.04570.06010.02190.0139-0.01040.15760.0137-0.01240.1583-0.01980.0967-1.96851.573-22.886
20.6781-0.0962-0.42640.38190.22910.39410.0251-0.02560.0504-0.00910.0818-0.1164-0.0123-0.0144-0.1070.1441-0.02520.01560.1486-0.04530.1223-11.93681.647-7.778
31.50880.5605-0.6991.44690.03760.4007-0.09220.05680.0225-0.08170.1587-0.28050.0286-0.0049-0.06650.1113-0.04810.04690.062-0.08230.3048-9.681114.1172.196
41.3812-0.95320.68761.5129-0.18930.44890.0229-0.1097-0.4797-0.15740.15760.5217-0.0455-0.0059-0.18050.0489-0.044-0.08730.05160.07850.4521-9.93219.52-14.301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 259
2X-RAY DIFFRACTION1A901 - 915
3X-RAY DIFFRACTION1A1001 - 1132
4X-RAY DIFFRACTION2B1 - 259
5X-RAY DIFFRACTION2B901 - 921
6X-RAY DIFFRACTION2B1001 - 1115
7X-RAY DIFFRACTION3C0 - 259
8X-RAY DIFFRACTION3C901 - 908
9X-RAY DIFFRACTION3C1001 - 1046
10X-RAY DIFFRACTION4D1 - 259
11X-RAY DIFFRACTION4D901 - 904
12X-RAY DIFFRACTION4D1001 - 1033

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