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- PDB-7cii: Crystal structure of L-methionine decarboxylase from Streptomyces... -

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Basic information

Entry
Database: PDB / ID: 7cii
TitleCrystal structure of L-methionine decarboxylase from Streptomyces sp.590 in complexed with L- methionine methyl ester (external aldimine form).
ComponentsL-methionine decarboxylase
KeywordsLYASE / decarboxylase / PLP-Dependent Enzymes
Function / homology: / carboxy-lyase activity / biosynthetic process / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Chem-G06 / L-methionine decarboxylase
Function and homology information
Biological speciesStreptomyces sp. 590 KI-2014 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsOkawa, A. / Shiba, T. / Hayashi, M. / Onoue, Y. / Murota, M. / Sato, D. / Inagaki, J. / Tamura, T. / Harada, S. / Inagaki, K.
CitationJournal: Protein Sci. / Year: 2021
Title: Structural basis for substrate specificity of l-methionine decarboxylase.
Authors: Okawa, A. / Shiba, T. / Hayashi, M. / Onoue, Y. / Murota, M. / Sato, D. / Inagaki, J. / Tamura, T. / Harada, S. / Inagaki, K.
History
DepositionJul 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-methionine decarboxylase
B: L-methionine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7394
Polymers122,9542
Non-polymers7852
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-63 kcal/mol
Surface area36520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.322, 147.588, 54.011
Angle α, β, γ (deg.)90.00, 99.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein L-methionine decarboxylase


Mass: 61477.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. 590 KI-2014 (bacteria)
Plasmid: pET-52b / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G4DBU7, EC: 4.1.1.57
#2: Chemical ChemComp-G06 / methyl (2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-4-methylsulfanyl-butanoate


Mass: 392.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MMT buffer pH 6.0, 23.5 % (w/v) PEG1500 / PH range: 5.6-6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 25, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 143471 / % possible obs: 97.9 % / Redundancy: 2.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.117 / Net I/σ(I): 6.5
Reflection shellResolution: 1.51→1.6 Å / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 46587 / CC1/2: 0.623 / Rpim(I) all: 0.885 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CIF

7cif


Resolution: 1.51→19.91 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.569 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19567 7493 5 %RANDOM
Rwork0.17427 ---
obs0.17534 143070 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.981 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.51→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8134 0 50 471 8655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198549
X-RAY DIFFRACTIONr_bond_other_d0.0030.027892
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.96511668
X-RAY DIFFRACTIONr_angle_other_deg0.9923.00118161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89751059
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88122.854403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.761151291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9221576
X-RAY DIFFRACTIONr_chiral_restr0.0950.21217
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219808
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022008
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_it1.4691.9714218
X-RAY DIFFRACTIONr_mcbond_other1.4691.9714217
X-RAY DIFFRACTIONr_mcangle_it2.532.9465283
X-RAY DIFFRACTIONr_mcangle_other2.5292.9465284
X-RAY DIFFRACTIONr_scbond_it1.8612.1664330
X-RAY DIFFRACTIONr_scbond_other1.8612.1664331
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0513.1796385
X-RAY DIFFRACTIONr_long_range_B_refined4.60415.62110035
X-RAY DIFFRACTIONr_long_range_B_other4.56315.4849862
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 500 -
Rwork0.422 10354 -
obs--98.02 %

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