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

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Basic information

Entry
Database: PDB / ID: 7cim
TitleCrystal structure of L-methionine decarboxylase from Streptomyces sp.590 in complexed with 3-methlythiopropylamine (geminal diamine form).
ComponentsL-methionine decarboxylase
KeywordsLYASE / decarboxylase / PLP-Dependent Enzymes
Function / homologyPyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Chem-G0F / L-methionine decarboxylase
Function and homology information
Biological speciesStreptomyces sp. 590 KI-2014 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.2Nov 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)123,6274
Polymers122,9542
Non-polymers6732
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-61 kcal/mol
Surface area38120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.639, 147.813, 54.187
Angle α, β, γ (deg.)90.00, 99.47, 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-G0F / [6-methyl-4-[(3-methylsulfanylpropylamino)methyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate


Mass: 336.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H21N2O5PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.15 Å3/Da / Density % sol: 42.66 %
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: Jun 27, 2019
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: 88135 / % possible obs: 98.1 % / Redundancy: 2.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.084 / Net I/σ(I): 8.3
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2 / Num. unique obs: 27664 / CC1/2: 0.87 / Rpim(I) all: 0.519 / % possible all: 95.9

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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: 1.8→19.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.007 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23798 4496 5 %RANDOM
Rwork0.2027 ---
obs0.20444 85096 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.918 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8160 0 42 271 8473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198455
X-RAY DIFFRACTIONr_bond_other_d0.0030.027800
X-RAY DIFFRACTIONr_angle_refined_deg1.461.96311522
X-RAY DIFFRACTIONr_angle_other_deg1.0093.00117950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55751040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35222.947397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.587151267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4951572
X-RAY DIFFRACTIONr_chiral_restr0.0980.21207
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219640
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021982
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_it2.1733.4694171
X-RAY DIFFRACTIONr_mcbond_other2.173.4674169
X-RAY DIFFRACTIONr_mcangle_it3.5545.1825206
X-RAY DIFFRACTIONr_mcangle_other3.5545.1845207
X-RAY DIFFRACTIONr_scbond_it2.4193.7224284
X-RAY DIFFRACTIONr_scbond_other2.4193.7224285
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9455.56317
X-RAY DIFFRACTIONr_long_range_B_refined6.11827.2959631
X-RAY DIFFRACTIONr_long_range_B_other6.11727.2779572
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 342 -
Rwork0.381 6026 -
obs--97.38 %

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