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

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Basic information

Entry
Database: PDB / ID: 7cif
TitleCrystal structure of L-methionine decarboxylase from Streptomyces sp.590 (internal 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 / L-methionine decarboxylase
Function and homology information
Biological speciesStreptomyces sp. 590 KI-2014 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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 1.2Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)123,4102
Polymers123,4102
Non-polymers00
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-64 kcal/mol
Surface area38010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.631, 147.499, 53.904
Angle α, β, γ (deg.)90.00, 99.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein L-methionine decarboxylase


Mass: 61705.215 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.98 Å3/Da / Density % sol: 37.8 %
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: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 86707 / % possible obs: 92.7 % / Redundancy: 1.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.077 / Net I/σ(I): 8.4
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 25929 / CC1/2: 0.665 / Rpim(I) all: 0.704 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.89 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.701 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23064 4308 5 %RANDOM
Rwork0.1897 ---
obs0.19174 82339 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.421 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8202 0 0 281 8483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198464
X-RAY DIFFRACTIONr_bond_other_d0.0020.027809
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.96411546
X-RAY DIFFRACTIONr_angle_other_deg1317966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33751045
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85922.879396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.386151259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4021573
X-RAY DIFFRACTIONr_chiral_restr0.0960.21210
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021984
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_it2.3173.4024186
X-RAY DIFFRACTIONr_mcbond_other2.3173.4014185
X-RAY DIFFRACTIONr_mcangle_it3.6185.0825229
X-RAY DIFFRACTIONr_mcangle_other3.6175.0845230
X-RAY DIFFRACTIONr_scbond_it2.7033.6744278
X-RAY DIFFRACTIONr_scbond_other2.7033.6744278
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2515.4216317
X-RAY DIFFRACTIONr_long_range_B_refined6.35426.9889665
X-RAY DIFFRACTIONr_long_range_B_other6.35326.9689608
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 289 -
Rwork0.357 5825 -
obs--94.21 %

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