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- PDB-4ho7: Crystal structure of eukaryotic HslV from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 4ho7
TitleCrystal structure of eukaryotic HslV from Trypanosoma brucei
ComponentsHslVU complex proteolytic subunit, putative
KeywordsHYDROLASE / mitochondria
Function / homology
Function and homology information


rolling circle DNA replication / HslU-HslV peptidase / mitochondrial DNA replication / HslUV protease complex / kinetoplast / nuclear lumen / ciliary plasm / proteasome core complex / ATP-dependent peptidase activity / mitochondrial nucleoid ...rolling circle DNA replication / HslU-HslV peptidase / mitochondrial DNA replication / HslUV protease complex / kinetoplast / nuclear lumen / ciliary plasm / proteasome core complex / ATP-dependent peptidase activity / mitochondrial nucleoid / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / endopeptidase activity / mitochondrion / cytoplasm
Similarity search - Function
ATP-dependent protease, HslV subunit / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent protease subunit HslV
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.601 Å
AuthorsSung, K.H. / Lee, S.Y. / Song, H.K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural and Biochemical Analyses of the Eukaryotic Heat Shock Locus V (HslV) from Trypanosoma brucei.
Authors: Sung, K.H. / Lee, S.Y. / Song, H.K.
History
DepositionOct 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HslVU complex proteolytic subunit, putative
B: HslVU complex proteolytic subunit, putative
C: HslVU complex proteolytic subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7656
Polymers58,6923
Non-polymers733
Water55831
1
A: HslVU complex proteolytic subunit, putative
B: HslVU complex proteolytic subunit, putative
C: HslVU complex proteolytic subunit, putative
hetero molecules

A: HslVU complex proteolytic subunit, putative
B: HslVU complex proteolytic subunit, putative
C: HslVU complex proteolytic subunit, putative
hetero molecules

A: HslVU complex proteolytic subunit, putative
B: HslVU complex proteolytic subunit, putative
C: HslVU complex proteolytic subunit, putative
hetero molecules

A: HslVU complex proteolytic subunit, putative
B: HslVU complex proteolytic subunit, putative
C: HslVU complex proteolytic subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,06124
Polymers234,77012
Non-polymers29212
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area32950 Å2
ΔGint-176 kcal/mol
Surface area71890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.673, 111.062, 116.953
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11C-313-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1 - 173 / Label seq-ID: 1 - 173

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein HslVU complex proteolytic subunit, putative


Mass: 19564.148 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb11.01.2000 / Production host: Escherichia coli (E. coli)
References: UniProt: Q383Q5, Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 3.5M Sodiumformate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 21375

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.601→33.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 24.685 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.543 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24805 1083 5.1 %RANDOM
Rwork0.20968 ---
obs0.21164 20054 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.783 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2---0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.601→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3930 0 3 31 3964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193966
X-RAY DIFFRACTIONr_bond_other_d0.0060.023948
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9675358
X-RAY DIFFRACTIONr_angle_other_deg0.98239048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9035516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50724.138174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32315723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9881539
X-RAY DIFFRACTIONr_chiral_restr0.0880.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024491
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02834
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A11088
12B11088
21A11091
22C11091
31B11097
32C11097
LS refinement shellResolution: 2.601→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.533 64 -
Rwork0.364 1443 -
obs--97.41 %
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)
11.63310.4086-0.12371.9338-0.02251.7101-0.07840.07220.1363-0.00260.06180.3934-0.1873-0.23850.01660.03460.05280.00210.13530.03890.09-16.057630.947854.7996
21.494-0.45650.04811.03340.23491.0701-0.09350.1518-0.117-0.33450.06870.3745-0.05160.02760.02480.1656-0.0208-0.13150.22630.0390.1424-16.213911.794330.268
31.66030.05360.42051.8953-0.50821.6793-0.0426-0.25480.09690.31420.22720.3822-0.1469-0.3077-0.18460.09760.06450.08640.18720.0430.1016-15.759718.802883.2159
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 173
2X-RAY DIFFRACTION1A200
3X-RAY DIFFRACTION2B1 - 173
4X-RAY DIFFRACTION2B200
5X-RAY DIFFRACTION3C1 - 173
6X-RAY DIFFRACTION3C200

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