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- PDB-3lz8: Structure of a putative chaperone dnaj from klebsiella pneumoniae... -

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Basic information

Entry
Database: PDB / ID: 3lz8
TitleStructure of a putative chaperone dnaj from klebsiella pneumoniae subsp. pneumoniae mgh 78578 at 2.9 a resolution.
ComponentsPutative chaperone DnaJ
KeywordsCHAPERONE / STRUCTURE GENOMICS / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


bent DNA binding / nucleoid / unfolded protein binding / protein folding / cytoplasm
Similarity search - Function
DNA-binding protein, curved-DNA / 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 ...DNA-binding protein, curved-DNA / 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
Curved DNA-binding protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Bearden, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of a Putative Chaperone Dnaj from Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 at 2.9 A Resolution.
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Bearden, J. / Joachimiak, A. / Anderson, W.F.
History
DepositionMar 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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
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: Putative chaperone DnaJ
B: Putative chaperone DnaJ


Theoretical massNumber of molelcules
Total (without water)74,4522
Polymers74,4522
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-38 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.886, 67.396, 136.818
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 Putative chaperone DnaJ


Mass: 37225.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: cbpA, KPN78578_44400, KPN_04509 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Magic / References: UniProt: A6TH30
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.92 Å3/Da / Density % sol: 35.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Bicine, 10% PEG6000, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 / Wavelength: 0.97872 Å
DetectorDetector: CCD / Date: Feb 3, 2010 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: MOLECULAR REPLACEMENT / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.85→68.36 Å / Num. all: 13972 / Num. obs: 13972 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 97.8 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 33.848
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.733 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0051refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I38

3i38


Resolution: 2.9→68.36 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.942 / SU B: 25.521 / SU ML: 0.363 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.014 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.268 654 4.9 %RANDOM
Rwork0.226 ---
obs0.228 13235 99.79 %-
all-13972 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--3.65 Å20 Å2
3----4.44 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: LAST / Resolution: 2.9→68.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 0 7 2833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222890
X-RAY DIFFRACTIONr_bond_other_d0.0010.021924
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9743945
X-RAY DIFFRACTIONr_angle_other_deg0.93834737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5945367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56424.545110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78915462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3611514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02519
X-RAY DIFFRACTIONr_mcbond_it0.9881.51857
X-RAY DIFFRACTIONr_mcbond_other0.1551.5746
X-RAY DIFFRACTIONr_mcangle_it1.8423005
X-RAY DIFFRACTIONr_scbond_it2.38531033
X-RAY DIFFRACTIONr_scangle_it4.0324.5940
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 47 -
Rwork0.313 922 -
obs-69 100 %
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)
14.955-0.37170.24612.8598-0.37945.661-0.41160.2299-0.36570.04580.1056-0.02010.0097-0.30090.3060.0963-0.09260.06590.1208-0.07450.0646-11.3272-3.672217.0679
25.2672-1.29672.18063.69310.167510.6999-0.16180.71330.3348-0.5347-0.4290.2009-1.74550.15450.59070.38890.0155-0.08310.128-0.00210.1053-7.78977.9546.1531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A198 - 302
2X-RAY DIFFRACTION2B198 - 302

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