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- PDB-4j4b: PylD in complex with L-lysine-Ne-D-ornithine and NADH -

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Basic information

Entry
Database: PDB / ID: 4j4b
TitlePylD in complex with L-lysine-Ne-D-ornithine and NADH
ComponentsPylD
KeywordsOXIDOREDUCTASE / Pyrrolysine / 22nd Amino Acid / Biosynthesis / Rossmann Fold / Dehydrogenase / NADH
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor / 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~6~-D-ornithyl-L-lysine / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Pyrrolysine synthase
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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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)57,70010
Polymers55,7532
Non-polymers1,9468
Water3,729207
1
A: PylD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8505
Polymers27,8771
Non-polymers9734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PylD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8505
Polymers27,8771
Non-polymers9734
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)115,39920
Polymers111,5074
Non-polymers3,89216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area11630 Å2
ΔGint-158 kcal/mol
Surface area39720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.383, 142.440, 167.305
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-425-

HOH

21B-426-

HOH

31B-438-

HOH

41B-444-

HOH

51B-469-

HOH

61B-543-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.506347, 0.01601, 0.862181), (-0.018087, -0.999805, 0.007943), (0.86214, -0.011572, 0.506538)-0.67394, 37.11193, 0.30283

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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 , 5 types, 215 molecules

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


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-0TF / N~6~-D-ornithyl-L-lysine


Mass: 260.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24N4O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS; 27% PEG3350; 0.2 M Li2SO4, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Dec 16, 2012
RadiationMonochromator: BRUKER MICROSTAR MICRO-FOCUS (MONTEL OPTICS) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→60 Å / Num. all: 46157 / Num. obs: 46111 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.7
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.7.0029refinement
PROTEUM PLUSPLUSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet-model; coordinates have not been deposited

Resolution: 1.9→10 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.472 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 2330 5.1 %RANDOM
Rwork0.20533 ---
all0.213 43739 --
obs0.20703 43739 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.879 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0 Å2
2---0.77 Å2-0 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 128 207 4239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194115
X-RAY DIFFRACTIONr_angle_refined_deg1.2032.0135592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2495516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63425.75160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65615658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8261510
X-RAY DIFFRACTIONr_chiral_restr0.0740.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213046
X-RAY DIFFRACTIONr_rigid_bond_restr1.56234114
X-RAY DIFFRACTIONr_sphericity_free30.454577
X-RAY DIFFRACTIONr_sphericity_bonded5.70854162
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 173 -
Rwork0.306 3042 -
obs--98.89 %
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)
10.1106-0.13770.17480.99570.02821.1977-0.1141-0.0130.18770.2488-0.1983-0.03140.0739-0.04590.31240.1388-0.0054-0.08980.0506-0.0560.3883-17.520134.6597-19.9403
20.28240.11790.26560.30820.00360.6614-0.00610.01160.00040.0729-0.01030.0052-0.0080.02940.01640.02980.0101-0.00320.1244-0.00090.0092-8.87712.4188-24.8037
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 259
2X-RAY DIFFRACTION1A901 - 903
3X-RAY DIFFRACTION1B301
4X-RAY DIFFRACTION2B1 - 259
5X-RAY DIFFRACTION2A904
6X-RAY DIFFRACTION2B302 - 304

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