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- PDB-4q3d: PylD cocrystallized with L-Ornithine-Nd-D-ornithine and NAD+ -

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Basic information

Entry
Database: PDB / ID: 4q3d
TitlePylD cocrystallized with L-Ornithine-Nd-D-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
N~5~-D-ornithyl-L-ornithine / NICOTINAMIDE-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)116,20426
Polymers111,8554
Non-polymers4,34922
Water7,764431
1
A: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,34910
Polymers27,9641
Non-polymers1,3859
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0136
Polymers27,9641
Non-polymers1,0495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9215
Polymers27,9641
Non-polymers9574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9215
Polymers27,9641
Non-polymers9574
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)58,36216
Polymers55,9282
Non-polymers2,43514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x+1/2,-y+1/2,-z-11
Buried area5750 Å2
ΔGint-67 kcal/mol
Surface area20960 Å2
MethodPISA
6
C: PYLD, pyrrolysine synthase
D: PYLD, pyrrolysine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,84210
Polymers55,9282
Non-polymers1,9148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-72 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.930, 259.320, 48.820
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(-0.986713, 0.16231, -0.007296), (-0.162322, -0.986737, 0.001109), (-0.007019, 0.002279, 0.999973)-22.4092, 124.38944, 15.70365
3given(0.531224, 0.160235, -0.831941), (0.093083, -0.987046, -0.130672), (-0.842102, -0.008023, -0.539258)-23.20126, 187.05309, -14.23158
4given(-0.541934, 0.034127, 0.839728), (0.033624, -0.997495, 0.062238), (0.839748, 0.061964, 0.539429)30.52693, 191.97804, -24.94151

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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, 453 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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-2YH / N~5~-D-ornithyl-L-ornithine


Type: L-peptide linking / Mass: 246.307 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22N4O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
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: Aug 14, 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→30 Å / Num. all: 57292 / Num. obs: 56937 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 14
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 4.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4Q39

4q39


Resolution: 2.2→10 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.12 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 2847 5 %RANDOM
Rwork0.17669 ---
obs0.17968 54089 99.38 %-
all-56936 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.932 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0 Å2-0 Å2
2--0.33 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7481 0 286 431 8198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197908
X-RAY DIFFRACTIONr_bond_other_d0.0010.027324
X-RAY DIFFRACTIONr_angle_refined_deg1.1772.01210787
X-RAY DIFFRACTIONr_angle_other_deg0.753316882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51951016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64225.793290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.238151155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0721513
X-RAY DIFFRACTIONr_chiral_restr0.0590.21269
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021647
X-RAY DIFFRACTIONr_rigid_bond_restr2.245315230
X-RAY DIFFRACTIONr_sphericity_free35.855188
X-RAY DIFFRACTIONr_sphericity_bonded31.621515334
LS refinement shellResolution: 2.2→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 198 -
Rwork0.235 3761 -
obs--99.72 %
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)
10.01470.00920.0190.0213-0.00190.0375-0.0011-0.00530.00390.0032-0.00310.00260.002-0.01270.00420.0914-0.0003-0.00320.0977-0.00310.0011-2.58278.322-1.073
20.0306-0.0009-0.01710.00030.00160.0136-0.00330.0085-0.00230.00010.0037-0.00020.00010.0144-0.00040.0948-0.0023-0.00060.0996-0.00250.0008-11.97148.588-16.966
30.11530.0089-0.0030.13350.02750.00750.00740.03390.1092-0.00630.0033-0.00440.00580.0094-0.01070.1039-0.0018-0.00520.10870.0070.1133-10.07111.077-9.745
40.01650.00790.01170.08170.00320.01730.0095-0.00890.0237-0.0083-0.01280.0144-0.01010.00990.00330.1125-0.00230.00470.1301-0.00360.097933.96114.062-21.868
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 259
2X-RAY DIFFRACTION1A901 - 909
3X-RAY DIFFRACTION1A1001 - 1189
4X-RAY DIFFRACTION2B2 - 259
5X-RAY DIFFRACTION2B901 - 905
6X-RAY DIFFRACTION2B1001 - 1169
7X-RAY DIFFRACTION3C12 - 259
8X-RAY DIFFRACTION3C901 - 904
9X-RAY DIFFRACTION3C1001 - 1038
10X-RAY DIFFRACTION4D4 - 259
11X-RAY DIFFRACTION4D901 - 904
12X-RAY DIFFRACTION4D1001 - 1035

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