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- PDB-4q39: PylD in complex with pyrrolysine and NADH -

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Basic information

Entry
Database: PDB / ID: 4q39
TitlePylD in complex with pyrrolysine and NADH
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / PYRROLYSINE / 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 1.1Apr 30, 2014Group: Non-polymer description
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,27815
Polymers55,9282
Non-polymers2,35113
Water3,729207
1
A: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2849
Polymers27,9641
Non-polymers1,3208
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9946
Polymers27,9641
Non-polymers1,0305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: PYLD, pyrrolysine synthase
hetero molecules

A: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,56818
Polymers55,9282
Non-polymers2,64116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area6060 Å2
ΔGint-71 kcal/mol
Surface area21120 Å2
MethodPISA
4
B: PYLD, pyrrolysine synthase
hetero molecules

B: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,98812
Polymers55,9282
Non-polymers2,06010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area5170 Å2
ΔGint-72 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.500, 142.720, 167.310
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-1008-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.509551, -0.003061, 0.860435), (-0.001055, -0.999991, -0.004182), (0.86044, -0.003039, 0.509543)-0.58199, 37.16099, 0.5418

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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, 220 molecules

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


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#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-PYL / PYRROLYSINE


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


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


Mass: 62.068 Da / Num. of mol.: 2 / 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.: 207 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
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: Feb 9, 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: 30027 / Num. obs: 29283 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 26.1
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 6.1 / % possible all: 99.4

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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 4J4H

4j4h


Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.19 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.231 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19756 1465 5 %RANDOM
Rwork0.16181 ---
obs0.16363 27817 97.52 %-
all-29282 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.043 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å20 Å2
2--0.97 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 155 207 4274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194139
X-RAY DIFFRACTIONr_bond_other_d0.0020.023933
X-RAY DIFFRACTIONr_angle_refined_deg1.4162.0185627
X-RAY DIFFRACTIONr_angle_other_deg0.78639089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7235516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61625.802162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95815662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7131510
X-RAY DIFFRACTIONr_chiral_restr0.0750.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02866
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 105 -
Rwork0.209 1995 -
obs--99.57 %
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)
10.41810.34080.30950.35530.04410.95130.02470.0119-0.00830.0638-0.0203-0.00090.00050.0273-0.00440.10350.03-0.01930.1411-0.0070.1046-8.7662.343-24.878
20.5827-0.52760.59390.6129-0.16272.1548-0.1164-0.10590.14570.17370.162-0.1161-0.0935-0.006-0.04560.08490.06460.02270.0678-0.04620.2807-17.66434.923-19.847
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 259
2X-RAY DIFFRACTION1A901 - 908
3X-RAY DIFFRACTION1A1001 - 1156
4X-RAY DIFFRACTION2B1 - 259
5X-RAY DIFFRACTION2B901 - 905
6X-RAY DIFFRACTION2B1001 - 1051

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