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- PDB-1sfs: 1.07 A crystal structure of an uncharacterized B. stearothermophi... -

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Basic information

Entry
Database: PDB / ID: 1sfs
Title1.07 A crystal structure of an uncharacterized B. stearothermophilus protein
ComponentsHypothetical protein
KeywordsStructural Genomics / unknown function / possible bacterial Lysozyme / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyRv2525c-like, glycoside hydrolase-like domain / Rv2525c-like, glycoside hydrolase-like domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / PHOSPHATE ION / Rbstp1166 protein
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.07 Å
AuthorsMinasov, G. / Brunzelle, J.S. / Shuvalova, L. / Moy, S.F. / Collart, F.R. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.07 A crystal structure of an uncharacterized B. stearothermophilus protein
Authors: Minasov, G. / Brunzelle, J.S. / Shuvalova, L. / Moy, S.F. / Collart, F.R. / Anderson, W.F.
History
DepositionFeb 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 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.name
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE RESIDUES 0 TO -23 ARE HIS TAG RESIDUES. THE SEQUENCE OF THE PROTEIN HAS NOT YET BEEN ...SEQUENCE RESIDUES 0 TO -23 ARE HIS TAG RESIDUES. THE SEQUENCE OF THE PROTEIN HAS NOT YET BEEN DEPOSITED IN ANY SEQUENCE REFERENCE DATABASE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0602
Polymers26,9651
Non-polymers951
Water6,557364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.319, 70.090, 74.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein


Mass: 26965.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: RBSTP1166 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P84136
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M Ammonium Phosphate, 20% PEG, 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 27, 2003
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.07→15 Å / Num. all: 90332 / Num. obs: 90332 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.53 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.24
Reflection shellResolution: 1.07→1.11 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 6.64 / Num. unique all: 7244 / % possible all: 73.7

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.07→15 Å / Num. parameters: 22495 / Num. restraintsaints: 32495 / Isotropic thermal model: Anisotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.1352 4521 -RANDOM
Rwork0.1016 ---
all-85811 --
obs-85811 89.8 %-
Displacement parametersBiso mean: 16.84 Å2
Refine analyzeNum. disordered residues: 205 / Occupancy sum hydrogen: 1570.71 / Occupancy sum non hydrogen: 1975.72
Refinement stepCycle: LAST / Resolution: 1.07→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 5 432 2478
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0276
X-RAY DIFFRACTIONs_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.035
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.012
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.035
X-RAY DIFFRACTIONs_approx_iso_adps0.085
LS refinement shellResolution: 1.07→1.11 Å
RfactorNum. reflection% reflection
Rwork0.151 --
obs-6876 69.91 %

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