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- PDB-8vcw: X-Ray Crystal Structure of the biotin synthase from B. obeum -

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Basic information

Entry
Database: PDB / ID: 8vcw
TitleX-Ray Crystal Structure of the biotin synthase from B. obeum
ComponentsBiotin synthase
KeywordsTRANSFERASE / biotin / iron sulfur cluster / desthiobiotin / radical SAM
Function / homology
Function and homology information


biotin synthase / biotin synthase activity / biotin biosynthetic process / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Biotin synthase/Biotin biosynthesis bifunctional protein BioAB / Biotin synthase / Biotin and Thiamin Synthesis associated domain / Biotin and thiamin synthesis-associated domain / Biotin and Thiamin Synthesis associated domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-DTB / : / Fe4 H S5 / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Biotin synthase
Similarity search - Component
Biological speciesBlautia obeum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsLachowicz, J.C. / Grove, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007491 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Discovery of a Biotin Synthase That Utilizes an Auxiliary 4Fe-5S Cluster for Sulfur Insertion.
Authors: Lachowicz, J.C. / Lennox-Hvenekilde, D. / Myling-Petersen, N. / Salomonsen, B. / Verkleij, G. / Acevedo-Rocha, C.G. / Caddell, B. / Gronenberg, L.S. / Almo, S.C. / Sommer, M.O.A. / Genee, H.J. / Grove, T.L.
History
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biotin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9818
Polymers36,3311
Non-polymers1,6507
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.209, 50.776, 161.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Biotin synthase


Mass: 36331.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Contains a 4 iron:5 sulfur cluster / Source: (gene. exp.) Blautia obeum (bacteria) / Gene: bioB, RUMOBE_02699 / Plasmid: pSGCHis / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5ZUL4, biotin synthase

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Non-polymers , 8 types, 426 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-Q46 / Fe4 H S5


Mass: 384.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4HS5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DTB / 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID / D-DESTHIOBIOTIN


Mass: 214.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N2O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.4uL protein plus 0.4 uL 100mM Bis-Tri pH 5.5, 25% PEG 3350, 0.2M NaCl equilibrated against a well of 0.5M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0,9793
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2022 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
101
297931
ReflectionResolution: 1.35→80.94 Å / Num. obs: 67982 / % possible obs: 96.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 11.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.036 / Rrim(I) all: 0.076 / Χ2: 1.05 / Net I/σ(I): 12
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2523 / CC1/2: 0.741 / Rpim(I) all: 0.304 / Rrim(I) all: 0.535 / Χ2: 1.17 / % possible all: 75

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→48.45 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1731 3252 4.79 %Random
Rwork0.1498 ---
obs0.151 67854 96.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.1 Å2
Refinement stepCycle: LAST / Resolution: 1.35→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 75 419 3019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162742
X-RAY DIFFRACTIONf_angle_d2.7633748
X-RAY DIFFRACTIONf_dihedral_angle_d8.163427
X-RAY DIFFRACTIONf_chiral_restr0.303431
X-RAY DIFFRACTIONf_plane_restr0.012479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.26031010.22742096X-RAY DIFFRACTION73
1.37-1.390.22261340.21852332X-RAY DIFFRACTION82
1.39-1.410.26911120.20932543X-RAY DIFFRACTION87
1.41-1.440.22361190.19632640X-RAY DIFFRACTION93
1.44-1.460.2131600.18722781X-RAY DIFFRACTION97
1.46-1.490.19211400.16842846X-RAY DIFFRACTION99
1.49-1.520.21041350.15662880X-RAY DIFFRACTION99
1.52-1.560.1751410.15492841X-RAY DIFFRACTION99
1.56-1.590.16141560.14652872X-RAY DIFFRACTION99
1.59-1.630.15851470.13852845X-RAY DIFFRACTION100
1.63-1.680.19211440.14122864X-RAY DIFFRACTION99
1.68-1.730.17971330.15312872X-RAY DIFFRACTION99
1.73-1.780.17241480.14262848X-RAY DIFFRACTION99
1.78-1.850.17731310.14792895X-RAY DIFFRACTION99
1.85-1.920.16991440.14472898X-RAY DIFFRACTION99
1.92-2.010.18541550.14592886X-RAY DIFFRACTION99
2.01-2.110.16461530.14642888X-RAY DIFFRACTION99
2.11-2.250.17161520.14822885X-RAY DIFFRACTION99
2.25-2.420.17791430.1482915X-RAY DIFFRACTION99
2.42-2.660.17991340.15882926X-RAY DIFFRACTION99
2.66-3.050.16631350.15722968X-RAY DIFFRACTION99
3.05-3.840.16011810.13832957X-RAY DIFFRACTION99
3.84-48.450.14771540.1323124X-RAY DIFFRACTION99

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