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- PDB-4j49: PylD holoenzyme soaked with L-lysine-Ne-D-ornithine -

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Basic information

Entry
Database: PDB / ID: 4j49
TitlePylD holoenzyme soaked with L-lysine-Ne-D-ornithine
ComponentsPylD
KeywordsOXIDOREDUCTASE / Pyrrolysine / 22nd Amino Acid / Biosynthesis / Rossmann Fold / Dehydrogenase / NAD / L-lysine-Ne-3R-methyl-D-ornithine
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-1J1 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE 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: 2013
Title: Structure and Reaction Mechanism of Pyrrolysine Synthase (PylD).
Authors: Quitterer, F. / Beck, P. / Bacher, A. / Groll, M.
History
DepositionFeb 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PylD
B: PylD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4189
Polymers55,7532
Non-polymers1,6657
Water3,351186
1
A: PylD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5874
Polymers27,8771
Non-polymers7113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PylD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8315
Polymers27,8771
Non-polymers9544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: PylD
hetero molecules

B: PylD
hetero molecules

A: PylD
hetero molecules

A: PylD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,83618
Polymers111,5074
Non-polymers3,32914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_653-x+1,y,-z-3/21
crystal symmetry operation6_544-x+1/2,-y-1/2,z-1/21
crystal symmetry operation8_544x+1/2,-y-1/2,-z-11
Buried area11880 Å2
ΔGint-122 kcal/mol
Surface area41350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.2800, 211.4500, 77.2600
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1066-

HOH

21A-1082-

HOH

31B-1064-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PylD


Mass: 27876.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina barkeri (archaea) / Strain: Fusaro / Gene: Mbar_A0835 / 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 , 6 types, 193 molecules

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


Mass: 663.425 Da / Num. of mol.: 1 / 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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#6: Chemical ChemComp-1J1 / N~6~-[(2R)-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]-L-lysine / pyrroline-carboxy-lysine / PCL


Mass: 241.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N3O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
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: Jun 24, 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→30 Å / Num. all: 34254 / Num. obs: 34220 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.5
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 6.7 / % possible all: 99.9

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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: SeMet-model; coordinates have not been deposited

Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.732 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20513 1711 5 %RANDOM
Rwork0.17232 ---
all0.178 32509 --
obs0.17394 32509 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.287 Å2
Baniso -1Baniso -2Baniso -3
1-3.54 Å20 Å2-0 Å2
2---2.89 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 109 186 4121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194009
X-RAY DIFFRACTIONr_angle_refined_deg1.1432.0115461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.795502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06925.696158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95215644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0281510
X-RAY DIFFRACTIONr_chiral_restr0.0710.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212974
X-RAY DIFFRACTIONr_rigid_bond_restr1.41434006
X-RAY DIFFRACTIONr_sphericity_free26.568574
X-RAY DIFFRACTIONr_sphericity_bonded6.83754047
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 122 -
Rwork0.204 2329 -
obs--99.92 %
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)
10.1123-0.18150.1541.26980.130.416-0.013-0.01960.0101-0.15160.0291-0.0856-0.09530.0255-0.01610.0497-0.01170.01760.0589-0.01380.019817.0727-17.1408-15.9502
20.0770.205-0.02261.91290.24260.27750.037-0.0059-0.0229-0.01260.0177-0.1197-0.0867-0.035-0.05470.05750.01060.02450.0544-0.00390.042630.3941-43.8804-44.2939
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 259
2X-RAY DIFFRACTION1A901 - 903
3X-RAY DIFFRACTION2B3 - 259
4X-RAY DIFFRACTION2B901 - 904

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