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- PDB-2p65: Crystal Structure of the first nucleotide binding domain of chape... -

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Basic information

Entry
Database: PDB / ID: 2p65
TitleCrystal Structure of the first nucleotide binding domain of chaperone ClpB1, putative, (Pv089580) from Plasmodium Vivax
ComponentsHypothetical protein PF08_0063
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ClpB / plasmodium / malaria / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


apicoplast / protein unfolding / cellular response to heat / protein refolding / mitochondrial matrix / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal ...ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chaperone protein ClpB1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWernimont, A.K. / Lew, J. / Kozieradzki, I. / Lin, Y.H. / Hassanali, A. / Zhao, Y. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. ...Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Lin, Y.H. / Hassanali, A. / Zhao, Y. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Artz, J.D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the first nucleotide binding domain of chaperone ClpB1, putative, (Pv089580) from Plasmodium Vivax
Authors: Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Lin, Y.H. / Hassanali, A. / Zhao, Y. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Artz, J.D.
History
DepositionMar 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein PF08_0063


Theoretical massNumber of molelcules
Total (without water)20,4401
Polymers20,4401
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.728, 52.213, 91.920
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 Hypothetical protein PF08_0063


Mass: 20439.584 Da / Num. of mol.: 1
Fragment: Putative nucleotide binding domain (Residues 190-480)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PV089580:Y168-S353 / Plasmid: p15-tev-lic / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Oxford / References: UniProt: Q8IB03
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.86 Å3/Da / Density % sol: 33.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.4 M Sodium Citrate 100 mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→92.06 Å / Num. all: 17611 / Num. obs: 16520 / % possible obs: 93.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Rsym value: 0.092 / Net I/σ(I): 19.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.08 / Num. unique all: 1167 / Rsym value: 0.325 / % possible all: 67.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JBK.pdb

1jbk


Resolution: 1.7→92.06 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.466 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23927 841 5.1 %RANDOM
Rwork0.20103 ---
all0.20295 16711 --
obs0.20295 15670 93.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.753 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2--1.35 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.7→92.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 0 139 1548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221422
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.9991913
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2085184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96223.44858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31515273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8271515
X-RAY DIFFRACTIONr_chiral_restr0.0730.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021037
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.2676
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.2995
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.541.5949
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82821465
X-RAY DIFFRACTIONr_scbond_it1.5723521
X-RAY DIFFRACTIONr_scangle_it2.5144.5448
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 42 -
Rwork0.339 781 -
obs-781 64.5 %

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