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- PDB-5v1s: Crystal structure of Streptococcus suis SuiB bound to S-adenosylm... -

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Basic information

Entry
Database: PDB / ID: 5v1s
TitleCrystal structure of Streptococcus suis SuiB bound to S-adenosylmethionine
ComponentsRadical SAM
KeywordsMETAL BINDING PROTEIN / Radical SAM enzyme / Lys-Trp crosslink / Streptococcus suis / metalloenzyme / SPASM domain / RRE domain
Function / homology
Function and homology information


catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Petide cyclisation enzyme, radical SAM / 4Fe4S-binding SPASM domain / Iron-sulfur cluster-binding 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
S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Radical SAM
Similarity search - Component
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.492 Å
AuthorsDavis, K.M. / Bacik, J.P. / Ando, N.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition.
Authors: Davis, K.M. / Schramma, K.R. / Hansen, W.A. / Bacik, J.P. / Khare, S.D. / Seyedsayamdost, M.R. / Ando, N.
History
DepositionMar 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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_asym_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.ptnr3_auth_asym_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Radical SAM
B: Radical SAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,99610
Polymers106,0892
Non-polymers2,9078
Water1267
1
A: Radical SAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4985
Polymers53,0451
Non-polymers1,4534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Radical SAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4985
Polymers53,0451
Non-polymers1,4534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.787, 85.473, 109.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Radical SAM


Mass: 53044.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Gene: ERS132399_01508 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Z8EWX1
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: A solution containing 18.9 mg/mL His6-tagged SuiB in in storage buffer [100 mM HEPES, pH 7.5, 300 mM KCl, 5 mM DTT, 10% (v/v) glycerol] was mixed 1:1 with precipitant solution. Small ...Details: A solution containing 18.9 mg/mL His6-tagged SuiB in in storage buffer [100 mM HEPES, pH 7.5, 300 mM KCl, 5 mM DTT, 10% (v/v) glycerol] was mixed 1:1 with precipitant solution. Small clusters of crystals were formed within 24 hrs. A seed stock was then produced by combining a single sitting well with 10 uL of reservoir solution and 10 uL of enzyme at 8 mg/mL, followed by brief vortexing. Following seeding, a resulting crystal was incubated in precipitant solution containing ~6 mM SAM for 30 min prior to transfer to cryosolution.The precipitant solution was 100 mM MES, pH 6.0, 15% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.49→29.47 Å / Num. obs: 38407 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.7
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2 / Num. unique all: 4234 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V1Q

5v1q


Resolution: 2.492→29.47 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.08
RfactorNum. reflection% reflection
Rfree0.2697 1714 4.47 %
Rwork0.2148 --
obs0.2172 38359 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.492→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6657 0 102 7 6766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086937
X-RAY DIFFRACTIONf_angle_d0.7999413
X-RAY DIFFRACTIONf_dihedral_angle_d12.912549
X-RAY DIFFRACTIONf_chiral_restr0.0281089
X-RAY DIFFRACTIONf_plane_restr0.0021175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4916-2.56490.36341280.34742975X-RAY DIFFRACTION99
2.5649-2.64760.391510.32283008X-RAY DIFFRACTION100
2.6476-2.74220.34111400.31023027X-RAY DIFFRACTION100
2.7422-2.85190.32781400.29463008X-RAY DIFFRACTION100
2.8519-2.98150.32481350.26993046X-RAY DIFFRACTION100
2.9815-3.13860.34691420.26633012X-RAY DIFFRACTION100
3.1386-3.3350.29891490.26263044X-RAY DIFFRACTION100
3.335-3.5920.3181450.23883038X-RAY DIFFRACTION100
3.592-3.95280.25961400.21893064X-RAY DIFFRACTION100
3.9528-4.5230.24331450.18353076X-RAY DIFFRACTION100
4.523-5.69170.21931420.17563117X-RAY DIFFRACTION100
5.6917-29.47330.23651570.17143230X-RAY DIFFRACTION100

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