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- PDB-1wom: Crystal structure of RsbQ -

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Basic information

Entry
Database: PDB / ID: 1wom
TitleCrystal structure of RsbQ
ComponentsSigma factor sigB regulation protein rsbQ
KeywordsSIGNALING PROTEIN / alpha/beta hydrolase
Function / homology
Function and homology information


pimelyl-[acyl-carrier protein] methyl ester esterase activity / biotin biosynthetic process
Similarity search - Function
Alpha/beta hydrolase family / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONIC ACID / S-1,2-PROPANEDIOL / Sigma factor SigB regulation protein RsbQ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKaneko, T. / Kumasaka, T. / Tanaka, N.
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal structures of RsbQ, a stress-response regulator in Bacillus subtilis
Authors: Kaneko, T. / Tanaka, N. / Kumasaka, T.
History
DepositionAug 21, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sigma factor sigB regulation protein rsbQ
B: Sigma factor sigB regulation protein rsbQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,40615
Polymers60,3892
Non-polymers1,01713
Water2,666148
1
A: Sigma factor sigB regulation protein rsbQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,98311
Polymers30,1941
Non-polymers78910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sigma factor sigB regulation protein rsbQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4234
Polymers30,1941
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.508, 82.404, 137.359
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 Sigma factor sigB regulation protein rsbQ / RsbQ


Mass: 30194.311 Da / Num. of mol.: 2 / Fragment: residues 5-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rsbq / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: O07015
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.5 Å3/Da / Density % sol: 65.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: sodium malonic acid, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 12, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→31.23 Å / Num. all: 31150 / Num. obs: 31002 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 47.4 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
CrystalClearV. 1.35 (MSC/RIGAKU)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→31.23 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1707875.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1519 4.9 %RANDOM
Rwork0.217 ---
obs0.217 30951 99.4 %-
all-31150 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.7629 Å2 / ksol: 0.335449 e/Å3
Displacement parametersBiso mean: 51.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.17 Å20 Å20 Å2
2--16.27 Å20 Å2
3----8.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→31.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4208 0 67 148 4423
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 218 4.3 %
Rwork0.263 4877 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMPROST.TOP
X-RAY DIFFRACTION3MLA.PARAM
X-RAY DIFFRACTION4PGQ.PARAM

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