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- PDB-1t6a: Crystal Structure of Protein of Unknown Function from Bacillus st... -

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Basic information

Entry
Database: PDB / ID: 1t6a
TitleCrystal Structure of Protein of Unknown Function from Bacillus stearothermophilus
ComponentsRBSTP2229 gene product
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / Bacillus stearothermophilus / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Rbstp2229 protein / Rbstp2229 like protein / Protein of unknown function DUF1885 / Rbstp2229-like superfamily / Domain of unknown function (DUF1885) / TATA-Binding Protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Rbstp2229 protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsOsipiuk, J. / Wu, R. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of hypothetical protein (RBSTP2229 gene product) from Bacillus stearothermophilus
Authors: Osipiuk, J. / Wu, R. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionMay 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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 / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence of the protein was not deposited into any sequence database.
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). The biological molecule for the protein is not known.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RBSTP2229 gene product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1962
Polymers14,1341
Non-polymers621
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.307, 77.307, 200.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-299-

HOH

21A-300-

HOH

Detailsthe biological assembly unknown

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Components

#1: Protein RBSTP2229 gene product


Mass: 14134.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P84137
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 4.1 Å3/Da / Density % sol: 69.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Bis-Tris-Propane, Sodium Nitrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97952 Å
DetectorType: SBC-2 / Detector: CCD / Date: Apr 12, 2004
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. all: 14861 / Num. obs: 14757 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 22.4
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.07 / Num. unique all: 1010 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→40 Å / Cor.coef. Fo:Fc: 0.953 / SU B: 2.831 / SU ML: 0.075 / σ(F): 0 / ESU R: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22462 746 -random
Rwork0.19429 ---
all0.19618 14754 --
obs0.19618 14008 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.926 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20.88 Å20 Å2
2--1.77 Å20 Å2
3----2.65 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 4 100 1101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221020
X-RAY DIFFRACTIONr_bond_other_d0.0020.02943
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.9651371
X-RAY DIFFRACTIONr_angle_other_deg1.30532201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6245123
X-RAY DIFFRACTIONr_chiral_restr0.070.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021109
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02208
X-RAY DIFFRACTIONr_nbd_refined0.1920.2171
X-RAY DIFFRACTIONr_nbd_other0.2310.2952
X-RAY DIFFRACTIONr_nbtor_other0.0810.2578
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.261
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.213
X-RAY DIFFRACTIONr_mcbond_it0.8341.5620
X-RAY DIFFRACTIONr_mcangle_it1.6392987
X-RAY DIFFRACTIONr_scbond_it2.5923400
X-RAY DIFFRACTIONr_scangle_it4.4354.5384
LS refinement shellResolution: 2.053→2.106 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.314 55
Rwork0.275 1051
obs-996

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