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- PDB-3ijt: Structural Characterization of SMU.440, a Hypothetical Protein fr... -

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Basic information

Entry
Database: PDB / ID: 3ijt
TitleStructural Characterization of SMU.440, a Hypothetical Protein from Streptococcus mutans
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / HYPOTHETICAL PROTEIN
Function / homologySTART domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Polyketide cyclase
Function and homology information
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.377 Å
AuthorsNan, J. / Brostromer, E. / Kristensen, O. / Su, X.-D.
CitationJournal: Plos One / Year: 2009
Title: Bioinformatics and structural characterization of a hypothetical protein from Streptococcus mutans: implication of antibiotic resistance
Authors: Nan, J. / Brostromer, E. / Liu, X.-Y. / Kristensen, O. / Su, X.-D.
History
DepositionAug 5, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 25, 2009ID: 2B79
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 20, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)34,8532
Polymers34,8532
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-7 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.400, 99.680, 45.290
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 Putative uncharacterized protein / SMU.440


Mass: 17426.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU.440 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DVN6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.0259.33
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2891vapor diffusion, hanging drop725% PEG 3350, 0.2M ammonium sulfate, 0.1M Tris-HCl pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
2892vapor diffusion, hanging drop725% PEG 3350, 0.2M ammonium sulfate, 0.1M Tris-HCl pH7.0, 2.0mM ethylmercury thiosalicylate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.095 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 4, 2004
RadiationMonochromator: asymmetrically cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.095 Å / Relative weight: 1
ReflectionResolution: 2.377→34.078 Å / Num. obs: 17129 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 50.51 Å2 / Rsym value: 0.038 / Net I/σ(I): 11.9
Reflection shellResolution: 2.377→2.47 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1662 / Rsym value: 0.308 / % possible all: 97

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.377→34.078 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.791 / SU ML: 1.61 / Isotropic thermal model: Isotropic / σ(F): 0.07 / Phase error: 27.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 826 5.03 %RANDOM
Rwork0.2108 15593 --
obs0.213 16419 92.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.054 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 115.14 Å2 / Biso mean: 55.625 Å2 / Biso min: 33.01 Å2
Baniso -1Baniso -2Baniso -3
1--8.7652 Å20 Å20 Å2
2--4.0048 Å20 Å2
3---4.7604 Å2
Refinement stepCycle: LAST / Resolution: 2.377→34.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2265 0 0 90 2355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062313
X-RAY DIFFRACTIONf_angle_d0.933127
X-RAY DIFFRACTIONf_chiral_restr0.065346
X-RAY DIFFRACTIONf_plane_restr0.004406
X-RAY DIFFRACTIONf_dihedral_angle_d19.276843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3767-2.52560.33341240.26662364X-RAY DIFFRACTION86
2.5256-2.72050.33141380.25212488X-RAY DIFFRACTION91
2.7205-2.99410.37741300.25262630X-RAY DIFFRACTION95
2.9941-3.42710.27741420.24242678X-RAY DIFFRACTION96
3.4271-4.31640.22641480.18942715X-RAY DIFFRACTION97
4.3164-34.08140.20931440.18572718X-RAY DIFFRACTION92

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