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- PDB-8p2b: Crystal structure of CbFMN4 domain 1 -

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Basic information

Entry
Database: PDB / ID: 8p2b
TitleCrystal structure of CbFMN4 domain 1
ComponentsClostridiaceae bacterium FMN4 domain 1
KeywordsFLAVOPROTEIN / multi-flavinylated protein / FMN / post-translational
Function / homologySufe protein. Chain: A - #20 / Sufe protein. Chain: A / Alpha-Beta Complex / Alpha Beta / FLAVIN MONONUCLEOTIDE
Function and homology information
Biological speciesClostridiaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRozeboom, H.J. / Fraaije, M.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bba Adv / Year: 2023
Title: Characterization of two bacterial multi-flavinylated proteins harboring multiple covalent flavin cofactors.
Authors: Tong, Y. / Rozeboom, H.J. / Loonstra, M.R. / Wijma, H.J. / Fraaije, M.W.
History
DepositionMay 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clostridiaceae bacterium FMN4 domain 1
B: Clostridiaceae bacterium FMN4 domain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0354
Polymers18,1222
Non-polymers9132
Water19811
1
A: Clostridiaceae bacterium FMN4 domain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5172
Polymers9,0611
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Clostridiaceae bacterium FMN4 domain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5172
Polymers9,0611
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.915, 124.915, 29.846
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Clostridiaceae bacterium FMN4 domain 1


Mass: 9061.036 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridiaceae bacterium (bacteria) / Production host: Escherichia coli #1/H766 (bacteria) / Strain (production host): NEB 10-beta
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.4 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.7 / Details: 3.4 M ammonium sulfate, 0.1 M bis-tris-propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.6→40.9 Å / Num. obs: 8547 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.052 / Rrim(I) all: 0.161 / Χ2: 1.03 / Net I/σ(I): 13.7
Reflection shellResolution: 2.6→2.72 Å / % possible obs: 100 % / Redundancy: 9.5 % / Rmerge(I) obs: 2.623 / Num. measured all: 10011 / Num. unique obs: 1052 / CC1/2: 0.526 / Rpim(I) all: 0.894 / Rrim(I) all: 2.773 / Χ2: 0.88 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→40.9 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 27.141 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21917 388 4.5 %RANDOM
Rwork0.18212 ---
obs0.18378 8151 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å2-0.86 Å2-0 Å2
2---1.73 Å20 Å2
3---5.61 Å2
Refinement stepCycle: 1 / Resolution: 2.6→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 60 11 1301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121306
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161181
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.6361777
X-RAY DIFFRACTIONr_angle_other_deg0.4631.5482758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4255162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.84652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.70210220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0550.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021446
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02198
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_it4.5875.678654
X-RAY DIFFRACTIONr_mcbond_other4.4395.683654
X-RAY DIFFRACTIONr_mcangle_it6.8258.491814
X-RAY DIFFRACTIONr_mcangle_other6.8388.501815
X-RAY DIFFRACTIONr_scbond_it4.8795.95652
X-RAY DIFFRACTIONr_scbond_other4.8645.955650
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.238.746964
X-RAY DIFFRACTIONr_long_range_B_refined8.8666.3131483
X-RAY DIFFRACTIONr_long_range_B_other8.85766.3071484
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 22 -
Rwork0.401 609 -
obs--100 %
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)
14.25180.2507-2.42312.079-0.12011.4778-0.1753-0.1633-0.3311-0.13470.0236-0.30630.16370.01840.15170.0596-0.04650.00810.0723-0.01040.3353-22.830645.0928-0.1926
25.0417-0.447-0.64580.404-0.16551.0515-0.09840.2086-0.6288-0.18960.02230.02240.1524-0.08120.07620.13080.00520.03440.0627-0.0180.2993.03658.1945-5.7875
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 101
2X-RAY DIFFRACTION2B1 - 101

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