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- PDB-2q2g: Crystal structure of dimerization domain of HSP40 from Cryptospor... -

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Basic information

Entry
Database: PDB / ID: 2q2g
TitleCrystal structure of dimerization domain of HSP40 from Cryptosporidium parvum, cgd2_1800
ComponentsHeat shock 40 kDa protein, putative (fragment)
KeywordsCHAPERONE / heat shock / cryptosporidium / parvum / malaria / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


unfolded protein binding / protein folding
Similarity search - Function
Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. ...Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Heat shock 40 kDa protein, putative
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWernimont, A.K. / Lew, J. / Lin, L. / Hassanali, A. / Kozieradzki, I. / Wasney, G. / Vedadi, M. / Walker, J.R. / Zhao, Y. / Schapira, M. ...Wernimont, A.K. / Lew, J. / Lin, L. / Hassanali, A. / Kozieradzki, I. / Wasney, G. / Vedadi, M. / Walker, J.R. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Brokx, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of dimerization domain of HSP40 from Cryptosporidium parvum, cgd2_1800.
Authors: Wernimont, A.K. / Lew, J. / Lin, L. / Hassanali, A. / Kozieradzki, I. / Wasney, G. / Vedadi, M. / Walker, J.R. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Weigelt, J. / Sundstrom, M. / ...Authors: Wernimont, A.K. / Lew, J. / Lin, L. / Hassanali, A. / Kozieradzki, I. / Wasney, G. / Vedadi, M. / Walker, J.R. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Brokx, S.
History
DepositionMay 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock 40 kDa protein, putative (fragment)
B: Heat shock 40 kDa protein, putative (fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2394
Polymers41,0472
Non-polymers1922
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-32 kcal/mol
Surface area20520 Å2
MethodPISA
2
A: Heat shock 40 kDa protein, putative (fragment)
B: Heat shock 40 kDa protein, putative (fragment)
hetero molecules

A: Heat shock 40 kDa protein, putative (fragment)
B: Heat shock 40 kDa protein, putative (fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4798
Polymers82,0954
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6270 Å2
ΔGint-68 kcal/mol
Surface area39750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.480, 60.590, 48.830
Angle α, β, γ (deg.)90.00, 106.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Heat shock 40 kDa protein, putative (fragment) / HSP40 protein


Mass: 20523.641 Da / Num. of mol.: 2 / Fragment: Dimerization domain: Residues 102-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Species: Cryptosporidium parvum / Strain: Iowa type II / Gene: cgd2_1800 / Plasmid: p15_mhl / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: A3FQ69
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 19% PEG 3350, 0.2 M LiSO4, 0.1 M Bis-Tris pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D10.97926
SYNCHROTRONCHESS A120.9771
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDApr 15, 2007
ADSC QUANTUM 2102CCDApr 11, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.97711
ReflectionResolution: 1.9→50 Å / Num. all: 34983 / Num. obs: 34983 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 32.05 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.075 / Net I/σ(I): 12.61
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.13 / Num. unique all: 9519 / Rsym value: 0.388 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→30 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2909 1733 -random
Rwork0.2488 ---
obs0.2488 34859 97.8 %-
all-36060 --
Displacement parametersBiso mean: 35.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å2-0.58 Å2
2--4.34 Å20 Å2
3----2.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 10 286 2979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.316 266 -
Rwork0.279 --
obs-4603 81.6 %

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