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- PDB-3t7v: Crystal structure of methylornithine synthase (PylB) -

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Basic information

Entry
Database: PDB / ID: 3t7v
TitleCrystal structure of methylornithine synthase (PylB)
Componentsmethylornithine synthase PylB
KeywordsTRANSFERASE / TIM-barrel fold / Mutase / [4Fe-4S]-cluster / SAM / Lysine / 3-Methylornithine
Function / homology
Function and homology information


methylornithine synthase / pyrrolysine biosynthetic process / intramolecular transferase activity / transferase activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Pyrrolysine biosynthesis protein PylB / HydE/PylB-like / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Pyrrolysine biosynthesis protein PylB / HydE/PylB-like / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-amino-D-isoleucine / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / 3-methylornithine synthase
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsQuitterer, F. / List, A. / Eisenreich, W. / Bacher, A. / Groll, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Crystal structure of methylornithine synthase (PylB): insights into the pyrrolysine biosynthesis.
Authors: Quitterer, F. / List, A. / Eisenreich, W. / Bacher, A. / Groll, M.
History
DepositionJul 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_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_label_atom_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.value / _struct_conn.pdbx_dist_value / _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_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: methylornithine synthase PylB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9524
Polymers40,0561
Non-polymers8963
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.020, 77.020, 104.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-360-

HOH

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Components

#1: Protein methylornithine synthase PylB


Mass: 40055.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: joined expression with the plasmid pACYC184iscS-fdx necessary for biosynthesis of [4FE-4S]-cluster
Source: (gene. exp.) Methanosarcina barkeri (archaea) / Strain: Fusaro / DSM 804 / Gene: Mbar_A0838 / Plasmid: pET28b:SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: Q46E78, biotin synthase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-MD0 / 5-amino-D-isoleucine


Type: D-peptide linking / Mass: 146.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris-hydrochloride, 200 mM MgCl2, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2011
RadiationMonochromator: Fixed exit double, channel DCM Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 58172 / Num. obs: 58074 / % possible obs: 99.8 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 5.4 % / Rmerge(I) obs: 0.071 / Rsym value: 0.079 / Net I/σ(I): 12.6
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.525 / % possible all: 99.9

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→10 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.977 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16504 2904 5 %RANDOM
Rwork0.12865 ---
obs0.13049 55170 99.83 %-
all-57839 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.247 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2699 0 45 315 3059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192804
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5762.0163828
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.965336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16523.676136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87215510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3081527
X-RAY DIFFRACTIONr_chiral_restr0.2890.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212096
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4181.51683
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.52922713
X-RAY DIFFRACTIONr_scbond_it3.18831115
X-RAY DIFFRACTIONr_scangle_it4.9634.51055
X-RAY DIFFRACTIONr_rigid_bond_restr8.31232802
X-RAY DIFFRACTIONr_sphericity_free36.2595101
X-RAY DIFFRACTIONr_sphericity_bonded14.84752963
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 199 -
Rwork0.161 3718 -
obs--99.77 %
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)
12.12191.4642-1.92741.0135-1.33291.75440.3563-0.3783-0.00180.2763-0.30390.0149-0.35780.3388-0.05240.1772-0.11080.04240.1565-0.01760.091644.207845.991128.9195
20.24130.1358-0.24930.34780.09980.47970.04540.04530.07810.01050.03260.0632-0.046-0.0186-0.0780.10220.00610.01940.09720.00870.10246.2545.55629.4658
30.28940.1652-0.1340.2517-0.03520.141-0.01930.0281-0.02020.02130.0291-0.03260.001-0.0075-0.00980.1104-0.0135-0.00010.108-0.00530.093657.82733.5713-1.0695
40.3160.8319-0.31682.2931-0.88180.34030.0243-0.0515-0.06590.1032-0.0557-0.1013-0.04360.00660.03150.1211-0.0006-0.01550.14540.02590.107555.876427.128312.5373
50.79790.03-0.28790.0567-0.04910.1480.01-0.01040.01830.06150.00280.0015-0.014-0.0016-0.01280.1247-0.00670.00240.1179-0.0090.100149.630834.400515.3123
60.33170.10460.37050.08480.27671.0723-0.0260.02970.090.0216-0.00590.0257-0.0233-0.08430.03190.0965-0.01030.00440.1310.00460.097640.85937.00552.2791
70.4370.2351-0.30160.41330.0340.34360.10330.03930.13110.087-0.01130.0809-0.0461-0.0462-0.09210.11220.0070.02540.1015-0.00250.108142.893146.033810.519
80.3860.3218-0.13490.640.02260.09740.03770.06940.08790.01360.01420.0516-0.0208-0.04-0.05190.10870.01010.00910.09610.0230.11351.739250.0544-0.5622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 29
2X-RAY DIFFRACTION2A30 - 80
3X-RAY DIFFRACTION3A81 - 188
4X-RAY DIFFRACTION4A189 - 195
5X-RAY DIFFRACTION5A196 - 232
6X-RAY DIFFRACTION6A233 - 247
7X-RAY DIFFRACTION7A248 - 295
8X-RAY DIFFRACTION8A296 - 348
9X-RAY DIFFRACTION8A991 - 993

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