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- PDB-4j43: PylD holoenzyme -

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Basic information

Entry
Database: PDB / ID: 4j43
TitlePylD holoenzyme
ComponentsPylD
KeywordsOXIDOREDUCTASE / Pyrrolysine / 22nd Amino Acid / Biosynthesis / Rossmann Fold / Dehydrogenase / NAD
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
NICOTINAMIDE-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
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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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
B: PylD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1758
Polymers55,7532
Non-polymers1,4216
Water3,171176
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)28,5874
Polymers27,8771
Non-polymers7113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: PylD
hetero molecules

A: PylD
hetero molecules

B: PylD
hetero molecules

B: PylD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,35016
Polymers111,5074
Non-polymers2,84312
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 area10090 Å2
ΔGint-95 kcal/mol
Surface area42240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.980, 211.880, 77.620
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
11B-1033-

HOH

21B-1062-

HOH

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Components

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


Mass: 663.425 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
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: 2.94 Å3/Da / Density % sol: 58.15 %
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: May 14, 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: 34382 / Num. obs: 34176 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.3
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 6 / % possible all: 99.1

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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: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 9.624 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20127 1709 5 %RANDOM
Rwork0.16895 ---
all0.18 32467 --
obs0.17059 32467 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.27 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å20 Å2-0 Å2
2---2.17 Å2-0 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 92 176 4078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193985
X-RAY DIFFRACTIONr_angle_refined_deg1.1442.0065418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.785500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78525.696158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09815640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.591510
X-RAY DIFFRACTIONr_chiral_restr0.0750.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212958
X-RAY DIFFRACTIONr_rigid_bond_restr1.0433982
X-RAY DIFFRACTIONr_sphericity_free21.006580
X-RAY DIFFRACTIONr_sphericity_bonded6.16853998
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 122 -
Rwork0.216 2315 -
obs--99.11 %
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)
10.0710.0150.01881.24890.12590.31450.0471-0.02630.0102-0.0183-0.0073-0.056-0.0424-0.0208-0.03980.0606-0.00060.03320.02390.00330.029530.1067-43.755-44.0721
20.1148-0.11040.13881.09270.08540.3775-0.0258-0.0242-0.0024-0.11190.0308-0.0819-0.09030.0228-0.0050.0491-0.01260.02220.0306-0.00990.031417.0774-17.3481-15.9904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 259
2X-RAY DIFFRACTION1A901 - 903
3X-RAY DIFFRACTION2B4 - 259
4X-RAY DIFFRACTION2B901 - 903

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