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- PDB-1r30: The Crystal Structure of Biotin Synthase, an S-Adenosylmethionine... -

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Basic information

Entry
Database: PDB / ID: 1r30
TitleThe Crystal Structure of Biotin Synthase, an S-Adenosylmethionine-Dependent Radical Enzyme
ComponentsBiotin synthase
KeywordsTRANSFERASE / SAM Radical protein / TIM barrel / FeS cluster
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 ...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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-DTB / FE2/S2 (INORGANIC) CLUSTER / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Biotin synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.4 Å
AuthorsBerkovitch, F. / Nicolet, Y. / Wan, J.T. / Jarrett, J.T. / Drennan, C.L.
CitationJournal: Science / Year: 2004
Title: Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme.
Authors: Berkovitch, F. / Nicolet, Y. / Wan, J.T. / Jarrett, J.T. / Drennan, C.L.
History
DepositionSep 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biotin synthase
B: Biotin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,12811
Polymers82,7252
Non-polymers2,4029
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-100 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.690, 155.690, 90.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer containing both chains A and B

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Biotin synthase / Biotin synthetase


Mass: 41362.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BIOB / Plasmid: pET21d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P12996, biotin synthase

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Non-polymers , 5 types, 9 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical ChemComp-DTB / 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID / D-DESTHIOBIOTIN


Mass: 214.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N2O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM

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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: 3.84 Å3/Da / Density % sol: 67.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Tris, MgCl2, PEG 1000, Glycine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
225 mMTris-HCl1droppH8.0
30.1 MTris-HCl1reservoir
40.1 Mglycine1reservoir
50.2 M1reservoirMgCl2
620 %(w/v)PEG10001reservoirpH6.5
72.5 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.30000, 1.73827, 1.74150
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.31
21.738271
31.74151
ReflectionResolution: 3.4→50 Å / Num. all: 17465 / Num. obs: 17465 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rsym value: 0.066 / Net I/σ(I): 15.79
Reflection shellResolution: 3.4→3.51 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.78 / Num. unique all: 1416 / Rsym value: 0.244 / % possible all: 79.9
Reflection
*PLUS
Lowest resolution: 100 Å / % possible obs: 98.1 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 87.9 % / Rmerge(I) obs: 0.259

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Processing

Software
NameVersionClassification
CNS1refinement
CBASSdata collection
Adxvdata processing
XDSdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.4→44.45 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was refined with strict NCS constraints for the first stages of refinement. This was converted into strong NCS restraints during the last stages
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1242 7.1 %RANDOM
Rwork0.256 ---
obs0.256 17464 98.2 %-
all-17464 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 136.603 Å2 / ksol: 0.34188 e/Å3
Displacement parametersBiso mean: 90.6 Å2
Baniso -1Baniso -2Baniso -3
1-17.51 Å213.46 Å20 Å2
2--17.51 Å20 Å2
3----35.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.88 Å0.86 Å
Refinement stepCycle: LAST / Resolution: 3.4→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4866 0 116 0 4982
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.97
Refine LS restraints NCSNCS model details: RESTREINT
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 182 6.7 %
Rwork0.379 2539 -
obs-2539 93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CLUSTERS.PARAMCLUSTERS.TOP
X-RAY DIFFRACTION3LIGANDS_NEW.PARAMLIGANDS_NEW.TOP
Refinement
*PLUS
Highest resolution: 3.4 Å / Rfactor Rfree: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97

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