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- PDB-3i0t: Sulfur-SAD at long wavelength: Structure of BH3703 from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 3i0t
TitleSulfur-SAD at long wavelength: Structure of BH3703 from Bacillus halodurans
ComponentsBH3703 protein
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


BH3703-like domains / Immunity protein YezG-like / Immunity protein YezG-like superfamily / Immunity protein YezG-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle ...BH3703-like domains / Immunity protein YezG-like / Immunity protein YezG-like superfamily / Immunity protein YezG-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 Å
AuthorsRamagopal, U.A. / Toro, R. / Wasserman, S. / Burley, S.K. / Almo, S.C.
CitationJournal: To be published
Title: Sulfur-SAD at long wavelength: Structure of BH3703 from Bacillus halodurans
Authors: Ramagopal, U.A. / Toro, R. / Wasserman, S. / Burley, S.K. / Almo, S.C.
History
DepositionJun 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BH3703 protein
B: BH3703 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8953
Polymers43,7982
Non-polymers961
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-28 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.469, 81.474, 92.071
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BH3703 protein


Mass: 21899.232 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / JCM 9153 / Gene: BH3703 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K6M5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: (NH4)2SO4 2.0 M, Tris pH 7.5, LiSO4 0.2M, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 2.26864 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 26, 2006
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 2.26864 Å / Relative weight: 1
ReflectionResolution: 2.27→33.03 Å / % possible obs: 99.1 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.059 / Χ2: 1.154 / Net I/σ(I): 37.354
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.27-2.3560.19743570.72790.9
2.35-2.456.70.15348110.796100
2.45-2.566.90.12248050.889100
2.56-2.696.90.147920.984100
2.69-2.8670.08248391.145100
2.86-3.0870.06947951.321100
3.08-3.397.10.05848051.385100
3.39-3.8870.05447891.431100
3.88-4.897.30.0547991.363100
4.89-507.40.04948111.34599.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.27→33.03 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.211 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.849 / SU B: 4.821 / SU ML: 0.122 / SU R Cruickshank DPI: 0.252 / SU Rfree: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1289 5.1 %RANDOM
Rwork0.203 ---
obs0.205 25268 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.72 Å2 / Biso mean: 34.371 Å2 / Biso min: 16.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---2.03 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.27→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3011 0 5 189 3205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223128
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9184243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8865349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.19624.355186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3815508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.9931510
X-RAY DIFFRACTIONr_chiral_restr0.1020.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212518
X-RAY DIFFRACTIONr_mcbond_it0.8921.51743
X-RAY DIFFRACTIONr_mcangle_it1.74122820
X-RAY DIFFRACTIONr_scbond_it2.36531385
X-RAY DIFFRACTIONr_scangle_it3.8514.51423
LS refinement shellResolution: 2.27→2.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 85 -
Rwork0.321 1699 -
all-1784 -
obs--95.55 %

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