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- PDB-8p2a: Crystal structure of SaFMN3 domain 2 -

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Basic information

Entry
Database: PDB / ID: 8p2a
TitleCrystal structure of SaFMN3 domain 2
ComponentsFMN-binding domain-containing protein
KeywordsFLAVOPROTEIN / multi-flavinylated protein / FMN / post-translational
Function / homologyFMN-binding / FMN-binding domain / FMN_bind / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FMN binding / membrane / FLAVIN MONONUCLEOTIDE / FMN-binding domain-containing protein
Function and homology information
Biological speciesStreptomyces azureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Jul 26, 2023Group: Data collection / Database references / Category: citation / citation_author / pdbx_validate_planes
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 / _citation_author.name / _pdbx_validate_planes.type
Revision 1.2Jan 31, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMN-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4022
Polymers8,9461
Non-polymers4561
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint0 kcal/mol
Surface area4830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.954, 25.954, 364.838
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

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Components

#1: Protein FMN-binding domain-containing protein


Mass: 8945.968 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces azureus (bacteria) / Gene: SAZU_6878 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB 10-beta / References: UniProt: A0A0K8PVQ4
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 38 - 42 % PEG3350, 0.05 M bis-tris / PH range: 6.5 - 7.0

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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: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2→45.6 Å / Num. obs: 5999 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.039 / Rrim(I) all: 0.146 / Χ2: 0.79 / Net I/σ(I): 9 / Num. measured all: 78876
Reflection shellResolution: 2→2.05 Å / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 0.452 / Num. measured all: 4505 / Num. unique obs: 408 / CC1/2: 0.982 / Rpim(I) all: 0.137 / Rrim(I) all: 0.473 / Χ2: 0.37 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.42 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.4 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29763 260 4.4 %RANDOM
Rwork0.23097 ---
obs0.23395 5592 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.793 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 2→30.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms627 0 30 23 680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.012665
X-RAY DIFFRACTIONr_bond_other_d0.0010.016613
X-RAY DIFFRACTIONr_angle_refined_deg1.511.643904
X-RAY DIFFRACTIONr_angle_other_deg0.4741.561428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.062588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.203103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22810103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2108
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02109
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_it1.732.093355
X-RAY DIFFRACTIONr_mcbond_other1.7292.093355
X-RAY DIFFRACTIONr_mcangle_it2.4633.137442
X-RAY DIFFRACTIONr_mcangle_other2.4613.134443
X-RAY DIFFRACTIONr_scbond_it2.1922.386310
X-RAY DIFFRACTIONr_scbond_other2.1212.374308
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9073.494463
X-RAY DIFFRACTIONr_long_range_B_refined5.22430.063799
X-RAY DIFFRACTIONr_long_range_B_other5.1929.961797
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.478 10 -
Rwork0.264 389 -
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)
13.53140.3682-4.96881.7315-0.682913.02430.0510.0319-0.1156-0.0401-0.0778-0.12060.10970.69050.02680.13280.0356-0.03230.3937-0.05150.110410.0663-11.020210.466
24.14331.1528-3.23627.3511-7.119717.05230.00750.3394-0.3020.12330.20220.380.7116-0.8673-0.20970.142-0.0089-0.00020.3306-0.09910.0986-0.8029-13.639114.6141
37.38240.9274-5.30182.6304-0.610110.3510.35660.4250.46550.12190.0290.2048-0.9578-0.0888-0.38560.20180.01450.00880.3025-0.03320.06872.3827-5.978217.079
49.92045.21438.240521.6838-6.656413.2517-0.41411.20470.1686-0.4406-0.324-1.0896-0.32011.69550.73810.6021-0.29250.27790.97-0.18810.482615.0789-3.4339.0684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 36
2X-RAY DIFFRACTION2A37 - 63
3X-RAY DIFFRACTION3A64 - 83
4X-RAY DIFFRACTION4A84 - 89

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