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- PDB-3ucs: Crystal structure of the complex between CBPA J-domain and CBPM -

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Basic information

Entry
Database: PDB / ID: 3ucs
TitleCrystal structure of the complex between CBPA J-domain and CBPM
Components
  • Chaperone-modulator protein CbpM
  • Curved DNA-binding protein
KeywordsCHAPERONE / protein-protein complex / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / co-chaperone regulation
Function / homology
Function and homology information


bacterial nucleoid / bent DNA binding / chaperone cofactor-dependent protein refolding / unfolded protein binding / protein refolding / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
MerR HTH family regulatory protein / DNA-binding protein, curved-DNA / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / DnaJ domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site ...MerR HTH family regulatory protein / DNA-binding protein, curved-DNA / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / DnaJ domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / 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 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chaperone-modulator protein CbpM / Curved DNA-binding protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsShi, R. / Sarraf, N.S. / Cygler, M. / Ekiel, I. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: to be published
Title: Structure of the complex between CbpA J-domain and CbpM provides a link between chaperone and transcription regulation in bacterial heat shock response
Authors: Sarraf, N.S. / Shi, R. / Zhang, L. / Cygler, M. / Ekiel, I.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Chaperone-modulator protein CbpM
B: Chaperone-modulator protein CbpM
C: Curved DNA-binding protein
D: Curved DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)40,5624
Polymers40,5624
Non-polymers00
Water8,107450
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.816, 77.094, 111.231
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chaperone-modulator protein CbpM


Mass: 11432.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: 342 / Gene: cbpM, KPK_5158 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: B5Y388
#2: Protein Curved DNA-binding protein


Mass: 8847.874 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1000, cbpA, JW0985 / Plasmid: pMAL-c2X / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: P36659
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES pH 7.0, 20% PEG 8000, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorDetector: CCD / Date: Sep 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 38222 / % possible obs: 99.7 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.062 / Χ2: 1.087 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.87-1.947.60.48937140.984198.7
1.94-2.018.20.35237681.087199.9
2.01-2.118.20.23737671.14199.9
2.11-2.228.20.16837931.1231100
2.22-2.368.20.12737811.1581100
2.36-2.548.20.1138021.2431100
2.54-2.798.20.09338271.0591100
2.79-3.28.20.05938421.0051100
3.2-4.038.10.05438961.0291100
4.03-507.80.0340321.037198.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2447 / WRfactor Rwork: 0.2097 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8542 / SU B: 6.108 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1399 / SU Rfree: 0.1324 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 1911 5 %RANDOM
Rwork0.1959 ---
obs0.1977 38164 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 90.2 Å2 / Biso mean: 31.658 Å2 / Biso min: 14.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20 Å2
2--0.64 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.87→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 0 450 3240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222871
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9573903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6335348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96523.467150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19415510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6171531
X-RAY DIFFRACTIONr_chiral_restr0.0870.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212191
X-RAY DIFFRACTIONr_mcbond_it0.7441.51723
X-RAY DIFFRACTIONr_mcangle_it1.42422791
X-RAY DIFFRACTIONr_scbond_it2.22931148
X-RAY DIFFRACTIONr_scangle_it3.8014.51107
LS refinement shellResolution: 1.871→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 120 -
Rwork0.241 2593 -
all-2713 -
obs--98.12 %
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)
10.11810.06750.02760.0529-0.01160.1423-0.03140.0326-0.01410.00120.0032-0.0039-0.04940.00480.02820.0329-0.0118-0.00570.0459-0.02070.04042.3324-4.741-37.4405
20.18380.062-0.00140.1001-0.1030.1363-0.0045-0.0665-0.04380.0167-0.0339-0.0311-0.03750.03170.03840.0331-0.0097-0.02080.0674-0.00150.052718.949-1.2181-17.4236
31.5234-0.4346-0.57490.52830.3060.4939-0.0357-0.15240.03130.05020.03270.02130.03840.00120.00290.04160.00130.00910.0346-0.00180.0054-5.02625.2998-12.4177
41.8654-0.28760.18833.0866-0.06780.2509-0.07780.35940.1185-0.28970.0952-0.232-0.02270.0941-0.01740.0449-0.04870.02050.11130.00180.027221.57738.6535-42.9538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 100
2X-RAY DIFFRACTION2B2 - 101
3X-RAY DIFFRACTION3C0 - 73
4X-RAY DIFFRACTION4D3 - 71

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