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- PDB-1p3h: Crystal Structure of the Mycobacterium tuberculosis chaperonin 10... -

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Basic information

Entry
Database: PDB / ID: 1p3h
TitleCrystal Structure of the Mycobacterium tuberculosis chaperonin 10 tetradecamer
Components10 kDa chaperonin
KeywordsCHAPERONE / BETA BARREL / ACIDIC CLUSTER / FLEXIBLE LOOP / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


zymogen binding / cell wall / chaperone cofactor-dependent protein refolding / protein folding chaperone / peptidoglycan-based cell wall / unfolded protein binding / cellular response to heat / response to heat / protein-folding chaperone binding / response to antibiotic ...zymogen binding / cell wall / chaperone cofactor-dependent protein refolding / protein folding chaperone / peptidoglycan-based cell wall / unfolded protein binding / cellular response to heat / response to heat / protein-folding chaperone binding / response to antibiotic / regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular region / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
10 Kd Chaperonin, Protein Cpn10; Chain O / GroES chaperonin / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / GroES-like superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Co-chaperonin GroES / Co-chaperonin GroES
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRoberts, M.M. / Coker, A.R. / Fossati, G. / Mascagni, P. / Coates, A.R.M. / Wood, S.P. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: J.BACTERIOL. / Year: 2003
Title: Mycobacterium tuberculosis chaperonin 10 heptamers self-associate through their biologically active loops
Authors: Roberts, M.M. / Coker, A.R. / Fossati, G. / Mascagni, P. / Coates, A.R.M. / Wood, S.P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization, X-ray diffraction and preliminary structure analysis of Mycobacterium tuberculosis chaperonin 10
Authors: Roberts, M.M. / Coker, A.R. / Fossati, G. / Mascagni, P. / Coates, A.R.M. / Wood, S.P.
#2: Journal: J.EXP.MED. / Year: 1997
Title: Mycobacterium tuberculosis chaperonin 10 stimulates bone resorption: A potential contributory factor in Pott's Disease
Authors: Meghji, S. / White, P.A. / Nair, S.P. / Reddi, K. / Heron, K. / Henderson, B. / Zaliani, A. / Fossati, G. / Mascagni, P. / Hunt, J.F. / Roberts, M.M. / Coates, A.R.M.
History
DepositionApr 17, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionJul 15, 2003ID: 1JH2
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 10 kDa chaperonin
B: 10 kDa chaperonin
C: 10 kDa chaperonin
D: 10 kDa chaperonin
E: 10 kDa chaperonin
F: 10 kDa chaperonin
G: 10 kDa chaperonin
H: 10 kDa chaperonin
I: 10 kDa chaperonin
J: 10 kDa chaperonin
K: 10 kDa chaperonin
L: 10 kDa chaperonin
M: 10 kDa chaperonin
N: 10 kDa chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,75733
Polymers149,59014
Non-polymers2,16719
Water1,15364
1
A: 10 kDa chaperonin
B: 10 kDa chaperonin
C: 10 kDa chaperonin
D: 10 kDa chaperonin
E: 10 kDa chaperonin
F: 10 kDa chaperonin
G: 10 kDa chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,78016
Polymers74,7957
Non-polymers9859
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13240 Å2
ΔGint-148 kcal/mol
Surface area38690 Å2
MethodPISA
2
H: 10 kDa chaperonin
I: 10 kDa chaperonin
J: 10 kDa chaperonin
K: 10 kDa chaperonin
L: 10 kDa chaperonin
M: 10 kDa chaperonin
N: 10 kDa chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,97717
Polymers74,7957
Non-polymers1,18210
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12650 Å2
ΔGint-135 kcal/mol
Surface area39030 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45380 Å2
ΔGint-415 kcal/mol
Surface area58230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.460, 87.930, 124.390
Angle α, β, γ (deg.)90.00, 106.78, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
10 kDa chaperonin / Protein Cpn10 / groES protein / BCG-A heat shock protein / 10 kDa antigen


Mass: 10684.979 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: GROS OR GROES OR MOPB OR CPN10 OR RV3418C OR MT3527 OR MTCY78.11
Plasmid: pUC18 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P09621, UniProt: P9WPE5*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.67 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: MPD, sodium acetate, calcium chloride, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Details: Roberts, M.M., (1999) Acta Crystallogr.,Sect.D, 55, 910.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mM1reservoirCaCl2
20.1 Msodium acetate1reservoir
330 %MPD1reservoirpH5.4
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 8, 1996 / Details: mirrors
RadiationMonochromator: GERMANIUM CRYSTAL SET TO BRAGG REFLECTION (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 38321 / Num. obs: 38321 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 80.3 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 24.41
Reflection shellResolution: 2.8→2.82 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.92 / Num. unique all: 982 / Rsym value: 0.61 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 134674
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
XDSdata scaling
TRUNCATEdata reduction
DMmodel building
CNS1refinement
XDSdata reduction
CCP4(TRUNCATE)data scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE E.COLI GROES STRUCTURE WITH AMINO ACIDS DIFFERING FROM M.TUBERCULOSIS CHAPERONIN 10 TRUNCATED TO ALANINES

Resolution: 2.8→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Data cutoff high rms absF: 10000 / Isotropic thermal model: restrained
Cross valid method: TEST SET OF REFLECTIONS NOT USED IN REFINEMENT BUT TO MONITOR R-FREE
σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: RMS VALUES FOR NCS RELATED SUBUNITS APPLY TO ALL ATOMS IN EACH SUBUNIT. THE POSITIONAL NCS WEIGHTS INDICATED APPLY RESPECTIVELY TO MAINCHAIN (group 1) AND SIDECHAIN (group 2) ATOMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1900 5 %5% OF REFLECTIONS SELECTED IN THIN RESOLUTION SHELLS TO AVOID BIAS FROM NON-CRYSTALLOGRAPHIC SYMMETRY
Rwork0.259 ---
all0.26 36893 --
obs0.26 36893 94.3 %-
Solvent computationSolvent model: flat model / Bsol: 51.7 Å2 / ksol: 0.263 e/Å3
Displacement parametersBiso mean: 75.8 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å211.2 Å2
2---1.1 Å20 Å2
3---3.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.46 Å
Luzzati d res low-30 Å
Luzzati sigma a0.57 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10481 0 1 208 10690
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.991.5
X-RAY DIFFRACTIONc_mcangle_it4.762
X-RAY DIFFRACTIONc_scbond_it3.642
X-RAY DIFFRACTIONc_scangle_it5.242.5
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.398
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d0.97
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : 13.85 Å2 / Rms dev position: 1.33 Å / Weight Biso : 1

Ens-IDDom-IDNCS model detailsWeight position
11restraints applied to residues 6-30, 35-51, 55-81 and 83-99 in all subunits A-N50
2225
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 304 5.2 %
Rwork0.365 5527 -
obs-5527 90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3mpd.par (r-enantiomer)mpd.top (R-enantiomer)
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1

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