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- PDB-4it5: Chaperone HscB from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 4it5
TitleChaperone HscB from Vibrio cholerae
ComponentsCo-chaperone protein HscB homolog
KeywordsCHAPERONE / structural genomics / HscB / Hsc20 / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


iron-sulfur cluster transfer complex / protein maturation by iron-sulfur cluster transfer / [2Fe-2S] cluster assembly / ATPase activator activity / protein folding / protein complex oligomerization / protein-folding chaperone binding / cytosol / cytoplasm
Similarity search - Function
Co-chaperone Hsc20 / Co-chaperone HscB, C-terminal oligomerisation domain / HSCB C-terminal oligomerisation domain / HscB, C-terminal domain superfamily / HscB, C-terminal domain / DnaJ domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Monooxygenase ...Co-chaperone Hsc20 / Co-chaperone HscB, C-terminal oligomerisation domain / HSCB C-terminal oligomerisation domain / HscB, C-terminal domain superfamily / HscB, C-terminal domain / DnaJ domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Monooxygenase / Chaperone J-domain superfamily / DnaJ domain / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Co-chaperone protein HscB homolog
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.152 Å
AuthorsOsipiuk, J. / Gu, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Chaperone HscB from Vibrio cholerae.
Authors: Osipiuk, J. / Gu, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionJan 17, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJan 30, 2013ID: 3HHO
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Co-chaperone protein HscB homolog
B: Co-chaperone protein HscB homolog
C: Co-chaperone protein HscB homolog
D: Co-chaperone protein HscB homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1889
Polymers80,9874
Non-polymers2005
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-97 kcal/mol
Surface area37310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.430, 100.714, 70.346
Angle α, β, γ (deg.)90.000, 90.470, 90.000
Int Tables number4
Space group name H-MP1211
Detailsputative biological unit is either dimer or tetramer

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Components

#1: Protein
Co-chaperone protein HscB homolog /


Mass: 20246.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 / Gene: hscB, VC_0751 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KTX9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M calcium acetate, 0.1 M cacodylate buffer, 40% PEG-3000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→48.6 Å / Num. all: 41638 / Num. obs: 41638 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.094 / Χ2: 2.488 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.15-2.198.50.7722.4119351.19992.8
2.19-2.238.80.78220241.09195.9
2.23-2.2790.66220441.09798.5
2.27-2.329.30.52620821.13499.7
2.32-2.379.60.46120771.118100
2.37-2.429.80.40320921.133100
2.42-2.4810.10.33220771.103100
2.48-2.5510.10.28220941.144100
2.55-2.6210.10.24621001.171100
2.62-2.7110.10.21920671.186100
2.71-2.8110.50.19121101.312100
2.81-2.9215.10.22520911.499100
2.92-3.0515.20.16920851.507100
3.05-3.2115.20.13220861.656100
3.21-3.4115.20.120911.984100
3.41-3.68150.0821092.509100
3.68-4.05150.07220953.157100
4.05-4.6314.80.06921124.046100
4.63-5.8314.50.07321135.4100
5.83-5014.20.07321549.8999.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.152→48.56 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.7614 / SU ML: 0.29 / σ(F): 1.89 / σ(I): 0 / Phase error: 30.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 4126 5.07 %random
Rwork0.2198 ---
obs0.2218 41550 98.64 %-
all-81461 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127 Å2 / Biso mean: 61.1333 Å2 / Biso min: 26.72 Å2
Refinement stepCycle: LAST / Resolution: 2.152→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5373 0 5 91 5469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045455
X-RAY DIFFRACTIONf_angle_d0.7027350
X-RAY DIFFRACTIONf_chiral_restr0.047813
X-RAY DIFFRACTIONf_plane_restr0.002976
X-RAY DIFFRACTIONf_dihedral_angle_d18.9732086
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1518-2.17710.38921350.31232275241084
2.1771-2.20360.34511370.29352552268992
2.2036-2.23150.32151360.29062526266294
2.2315-2.26090.29311180.28412552267096
2.2609-2.29190.39521650.26952718288399
2.2919-2.32460.2921540.27212628278299
2.3246-2.35930.27771230.25927202843100
2.3593-2.39620.32971690.25427182887100
2.3962-2.43540.32441630.254626322795100
2.4354-2.47740.31031420.235726782820100
2.4774-2.52250.25981030.228127862889100
2.5225-2.5710.27081610.243626262787100
2.571-2.62350.3131440.2427472891100
2.6235-2.68050.3111360.233426552791100
2.6805-2.74290.27551500.246227462896100
2.7429-2.81140.29351140.246727212835100
2.8114-2.88750.30071310.246826952826100
2.8875-2.97240.2941520.24526932845100
2.9724-3.06830.35411110.261927542865100
3.0683-3.1780.31061700.252426192789100
3.178-3.30520.30911320.248327292861100
3.3052-3.45560.2861570.230626952852100
3.4556-3.63770.21751270.217827032830100
3.6377-3.86550.23611660.201227062872100
3.8655-4.16380.24311320.189226712803100
4.1638-4.58260.18791420.174827342876100
4.5826-5.2450.2131610.190326772838100
5.245-6.60550.29531420.230827002842100
6.6055-48.57210.20081530.18162679283299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.50220.9519-0.42510.6510.05110.27450.0122-0.0211-0.1105-0.0358-0.02930.0543-0.0529-0.0361-0.00060.30150.0094-0.00250.325-0.01960.334115.8705-3.231119.1225
20.2490.03860.25572.4813-0.30530.3037-0.0851-0.0140.05560.01550.2368-0.65190.105-0.061-0.00190.3956-0.0309-0.00370.3448-0.08650.388823.01774.4685-16.2918
32.31280.6030.51620.406-0.0250.18260.02560.07070.2029-0.0076-0.0324-0.01230.0514-0.02050.00070.2939-0.00670.02230.35630.03270.30911.660315.682319.0901
40.38290.0367-0.13422.37760.44780.2717-0.03180.06910.0713-0.08160.04730.7446-0.09190.0386-0.00020.4346-0.02260.01680.37870.06780.45474.7837.8748-16.4358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 170 )A0
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 170 )B0
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 170 )C0
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 170 )D0

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