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- PDB-1lep: THREE-DIMENSIONAL STRUCTURE OF THE IMMUNODOMINANT HEAT-SHOCK PROT... -

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Basic information

Entry
Database: PDB / ID: 1lep
TitleTHREE-DIMENSIONAL STRUCTURE OF THE IMMUNODOMINANT HEAT-SHOCK PROTEIN CHAPERONIN-10 OF MYCOBACTERIUM LEPRAE
ComponentsCHAPERONIN-10
KeywordsCHAPERONE / ANTIGEN / HEAT SHOCK
Function / homology
Function and homology information


protein folding / ATP binding / cytoplasm
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / GroES-like superfamily
Similarity search - Domain/homology
Biological speciesMycobacterium leprae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsMande, S.C. / Hol, W.G.J.
CitationJournal: Science / Year: 1996
Title: Structure of the heat shock protein chaperonin-10 of Mycobacterium leprae.
Authors: Mande, S.C. / Mehra, V. / Bloom, B.R. / Hol, W.G.
History
DepositionDec 13, 1995Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHAPERONIN-10
B: CHAPERONIN-10
C: CHAPERONIN-10
D: CHAPERONIN-10
E: CHAPERONIN-10
F: CHAPERONIN-10
G: CHAPERONIN-10


Theoretical massNumber of molelcules
Total (without water)74,7757
Polymers74,7757
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.900, 129.000, 109.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99951, 0.027091, -0.01567), (-0.029152, 0.62379, -0.781048), (-0.011385, 0.781122, 0.624275)-1.1535, 34.1533, -15.7811
2given(0.996091, 0.071494, -0.051885), (-0.032423, -0.250465, -0.967583), (-0.082172, 0.965482, -0.247167)-1.2586, 67.7524, 2.7868
3given(0.994807, -0.01047, -0.101236), (0.034269, -0.902154, 0.43005), (-0.095833, -0.431286, -0.897111)2.1245, 52.7986, 66.8419
4given(0.991862, 0.027411, -0.124331), (-0.026686, -0.910098, -0.413534), (-0.124489, 0.413486, -0.90196)2.7442, 75.4921, 38.7526
5given(0.992447, -0.045716, -0.113837), (0.101872, -0.209857, 0.972411), (-0.068344, -0.976663, -0.203614)3.9951, 12.9744, 67.0067
6given(0.996987, -0.060926, -0.048002), (0.076101, 0.648739, 0.757197), (-0.014992, -0.758569, 0.651421)3.2498, -10.731, 35.7531

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Components

#1: Protein
CHAPERONIN-10 / / ML10 / Coordinate model: Cα atoms only


Mass: 10682.150 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mycobacterium leprae (bacteria) / References: UniProt: P24301

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 55 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMMES1drop
21 mMEDTA1drop
31 mM1dropNaN3
4100 mMHEPES1reservoir
535 %(v/v)PEG4001reservoir
6150 mM1reservoirLiSO4

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRmerge(I) obs: 0.088
Reflection
*PLUS
Highest resolution: 3.5 Å / % possible obs: 98 %
Reflection shell
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 3.6 Å / % possible obs: 90 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 3.5→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.38 -
Rwork0.23 -
obs0.23 8733
Displacement parametersBiso mean: 40 Å2
Refinement stepCycle: LAST / Resolution: 3.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms567 0 0 0 567
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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