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- PDB-4jk3: PylD holoenzyme (SeMet) -

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Basic information

Entry
Database: PDB / ID: 4jk3
TitlePylD holoenzyme (SeMet)
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 / SAD / Resolution: 2.5 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
DepositionMar 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _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

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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)57,7388
Polymers56,3162
Non-polymers1,4216
Water88349
1
A: PylD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8694
Polymers28,1581
Non-polymers7113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PylD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8694
Polymers28,1581
Non-polymers7113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: PylD
B: PylD
hetero molecules

A: PylD
B: PylD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,47516
Polymers112,6324
Non-polymers2,84312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area10690 Å2
ΔGint-122 kcal/mol
Surface area41660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.650, 155.400, 39.570
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(-0.306636, 0.951004, -0.039582), (0.950911, 0.307899, 0.031084), (0.041749, -0.028108, -0.998733)103.15859, -74.2272, -57.93433

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Components

#1: Protein PylD


Mass: 28158.113 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
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2
References: Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor
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.: 49 / 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

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.43 %
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

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9798 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2012
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.8
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 21.626 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 1.033 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25659 887 5 %RANDOM
Rwork0.21559 ---
all0.221 16865 --
obs0.2176 16865 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.408 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å2-0 Å2-0 Å2
2---5.59 Å2-0 Å2
3---2.69 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 92 49 3939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193964
X-RAY DIFFRACTIONr_angle_refined_deg1.3612.0145402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3745498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58525.696158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.31715608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5651510
X-RAY DIFFRACTIONr_chiral_restr0.0890.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212950
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 62 -
Rwork0.258 1179 -
obs--100 %
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)
10.99411.1931-0.2181.8065-0.22950.51230.04760.022-0.07350.1022-0.0182-0.0457-0.02070.0018-0.02940.0188-0.0001-0.00690.1993-0.0180.024680.261227.5105-20.451
21.87262.77970.16495.1984-0.14450.176-0.3569-0.0113-0.2415-0.61420.3185-0.4964-0.0223-0.13460.03840.1477-0.06810.06260.1734-0.05320.0511105.30788.5089-33.3776
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 259
2X-RAY DIFFRACTION1A901 - 903
3X-RAY DIFFRACTION2B5 - 259
4X-RAY DIFFRACTION2B901 - 903

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