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- PDB-6j39: Crystal structure of CmiS2 with inhibitor -

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Basic information

Entry
Database: PDB / ID: 6j39
TitleCrystal structure of CmiS2 with inhibitor
ComponentsFAD-dependent glycine oxydase
KeywordsOXIDOREDUCTASE/INHIBITOR / Flavoenzyme / Polyketide biosynthesis / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


glycine oxidase / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / flavin adenine dinucleotide binding / oxidoreductase activity / cytoplasm
Similarity search - Function
Glycine oxidase ThiO / FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
(3R)-3-[(carboxymethyl)sulfanyl]nonanoic acid / FLAVIN-ADENINE DINUCLEOTIDE / glycine oxidase
Similarity search - Component
Biological speciesStreptomyces sp. MJ635-86F5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKawasaki, D. / Chisuga, T. / Miyanaga, A. / Kudo, F. / Eguchi, T.
CitationJournal: Biochemistry / Year: 2019
Title: Structural Analysis of the Glycine Oxidase Homologue CmiS2 Reveals a Unique Substrate Recognition Mechanism for Formation of a beta-Amino Acid Starter Unit in Cremimycin Biosynthesis.
Authors: Kawasaki, D. / Chisuga, T. / Miyanaga, A. / Kudo, F. / Eguchi, T.
History
DepositionJan 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD-dependent glycine oxydase
B: FAD-dependent glycine oxydase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5926
Polymers82,5242
Non-polymers2,0684
Water1,35175
1
A: FAD-dependent glycine oxydase
hetero molecules

B: FAD-dependent glycine oxydase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5926
Polymers82,5242
Non-polymers2,0684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area4250 Å2
ΔGint-31 kcal/mol
Surface area27050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.203, 84.013, 89.926
Angle α, β, γ (deg.)90.00, 97.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 2 - 368 / Label seq-ID: 22 - 388

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein FAD-dependent glycine oxydase


Mass: 41262.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. MJ635-86F5 (bacteria) / Gene: cmiS2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: X5IYZ1
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-B6X / (3R)-3-[(carboxymethyl)sulfanyl]nonanoic acid


Mass: 248.339 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES-Na, PEG3350, hexaamminecobalt(III) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 32256 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.8
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3633 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RYI

1ryi


Resolution: 2.45→44.36 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 13.418 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.434 / ESU R Free: 0.287 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27028 1630 5.1 %RANDOM
Rwork0.21355 ---
obs0.21641 30609 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.557 Å2
Baniso -1Baniso -2Baniso -3
1-9.68 Å2-0 Å23.08 Å2
2---4.92 Å2-0 Å2
3----4.99 Å2
Refinement stepCycle: 1 / Resolution: 2.45→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5333 0 138 75 5546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195581
X-RAY DIFFRACTIONr_bond_other_d0.0050.025461
X-RAY DIFFRACTIONr_angle_refined_deg1.4872.0167615
X-RAY DIFFRACTIONr_angle_other_deg1.0813.00212498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1255723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02722210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90915840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0981562
X-RAY DIFFRACTIONr_chiral_restr0.0720.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216277
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021187
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 21958 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 118 -
Rwork0.406 2255 -
obs--99.96 %

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