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- PDB-5wk0: Crystal structure of the bacillithiol transferase BstA from Staph... -

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Basic information

Entry
Database: PDB / ID: 5wk0
TitleCrystal structure of the bacillithiol transferase BstA from Staphylococcus aureus.
ComponentsDamage-inducible protein DinB
KeywordsUNKNOWN FUNCTION / bacillithiol / detoxification / helix bundle / metalloenzyme
Function / homologyDinB/YfiT-like putative metalloenzymes / transferase activity / NICKEL (II) ION / Bacillithiol transferase BstA / Bacillithiol transferase BstA
Function and homology information
Biological speciesStaphylococcus sp. HMSC055H04 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.335 Å
AuthorsCook, P.D. / Francis, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM117488 United States
CitationJournal: Protein Sci. / Year: 2018
Title: Structure and function of the bacillithiol-S-transferase BstA from Staphylococcus aureus.
Authors: Francis, J.W. / Royer, C.J. / Cook, P.D.
History
DepositionJul 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Damage-inducible protein DinB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7322
Polymers18,6731
Non-polymers591
Water2,270126
1
A: Damage-inducible protein DinB
hetero molecules

A: Damage-inducible protein DinB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4644
Polymers37,3472
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3440 Å2
ΔGint-50 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.019, 42.572, 50.414
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 Damage-inducible protein DinB


Mass: 18673.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus sp. HMSC055H04 (bacteria)
Gene: HMPREF2819_01945 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A1E8X683, UniProt: A0A2C9TMM3*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 1.9 Å3/Da / Density % sol: 35.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate trihydrate 20% (+/-) 2-methyl-2,4-dimethyl pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 1, 2017
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.335→50.4 Å / Num. obs: 32630 / % possible obs: 98.9 % / Redundancy: 7.7 % / CC1/2: 1 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.3
Reflection shellResolution: 1.335→1.34 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 319 / CC1/2: 0.82 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata processing
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CEX

3cex


Resolution: 1.335→32.526 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.38
RfactorNum. reflection% reflection
Rfree0.1895 1578 4.84 %
Rwork0.1505 --
obs0.1524 32580 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.335→32.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 1 126 1341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061314
X-RAY DIFFRACTIONf_angle_d0.7941804
X-RAY DIFFRACTIONf_dihedral_angle_d11.626748
X-RAY DIFFRACTIONf_chiral_restr0.071207
X-RAY DIFFRACTIONf_plane_restr0.005237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3353-1.37840.24381270.21322827X-RAY DIFFRACTION100
1.3784-1.42770.24451460.19712786X-RAY DIFFRACTION100
1.4277-1.48480.18651430.16512809X-RAY DIFFRACTION100
1.4848-1.55240.20581270.14172818X-RAY DIFFRACTION100
1.5524-1.63430.17031600.12732831X-RAY DIFFRACTION100
1.6343-1.73660.18511340.12522854X-RAY DIFFRACTION100
1.7366-1.87070.18391430.12852811X-RAY DIFFRACTION100
1.8707-2.05890.17371420.13492689X-RAY DIFFRACTION95
2.0589-2.35680.17831570.13392659X-RAY DIFFRACTION93
2.3568-2.9690.19181530.15672876X-RAY DIFFRACTION100
2.969-32.53590.19171460.15943042X-RAY DIFFRACTION100

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