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- PDB-2qas: Crystal structure of Caulobacter crescentus SspB ortholog -

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Basic information

Entry
Database: PDB / ID: 2qas
TitleCrystal structure of Caulobacter crescentus SspB ortholog
Components
  • C. crescentus ssrA peptide
  • Hypothetical protein
KeywordsHydrolase activator / sspB / adaptor / ClpX / ssrA / UNKNOWN FUNCTION
Function / homologySspB-like / Stringent starvation protein B / SspB-like superfamily / Stringent starvation protein B / SH3 type barrels. / Roll / Mainly Beta / identical protein binding / Stringent starvation protein B
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsChien, P. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
CitationJournal: To be Published
Title: Crystal structure of Caulobacter crescentus SspB ortholog
Authors: Chien, P. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
History
DepositionJun 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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: Hypothetical protein
B: C. crescentus ssrA peptide


Theoretical massNumber of molelcules
Total (without water)19,2512
Polymers19,2512
Non-polymers00
Water34219
1
A: Hypothetical protein
B: C. crescentus ssrA peptide

A: Hypothetical protein
B: C. crescentus ssrA peptide


Theoretical massNumber of molelcules
Total (without water)38,5034
Polymers38,5034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)121.760, 121.760, 27.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
DetailsBiological assembly is a dimer formed from the monomer in the asymmetric unit by the operations: -x,-y,z + [1,1,0]

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Components

#1: Protein Hypothetical protein / SspB


Mass: 17144.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Strain: CB15N / Gene: CC_2102 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9A6J2
#2: Protein/peptide C. crescentus ssrA peptide


Mass: 2107.285 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: synthetic ssrA pepitde with N-terminal solubilization tag
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4 M (NH4)2SO4, 0.1 M Tris, pH 8.0, hanging drop, temperature 300K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97908 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2006
RadiationMonochromator: crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 8146 / Num. obs: 7817 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.074 / Χ2: 1.161 / Net I/σ(I): 12.8
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.377 / Num. unique all: 653 / Χ2: 0.384 / % possible all: 85.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→26.76 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 85886.297 / 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
Rfree0.262 736 9.8 %RANDOM
Rwork0.213 ---
all0.218 8146 --
obs0.218 7531 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.361 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 69.4 Å2
Baniso -1Baniso -2Baniso -3
1--8.01 Å2-0.29 Å20 Å2
2---8.01 Å20 Å2
3---16.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.55→26.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 0 0 19 1027
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_mcbond_it2.091.5
X-RAY DIFFRACTIONc_mcangle_it3.812
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.532.5
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 94 8.9 %
Rwork0.29 964 -
obs-1058 80.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water.param

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