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- PDB-6w6r: WT HTLV-1 Protease in Complex with UMass6 (UM6) -

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Basic information

Entry
Database: PDB / ID: 6w6r
TitleWT HTLV-1 Protease in Complex with UMass6 (UM6)
ComponentsHTLV-1 Protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HTLV / PROTEASE / PROTEASE INHIBITOR / COMPLEX / HYDROLASE INHIBITOR COMPLEX / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Chem-A60 / Pro protein
Similarity search - Component
Biological speciesHuman T-cell leukemia virus type I
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLockbaum, G.J. / Henes, M. / Kosovrasti, K. / Nalivaika, E.A. / Ali, A. / KurtYilmaz, N. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01-GM109767 United States
CitationJournal: To Be Published
Title: To Be Determined
Authors: Lockbaum, G.J. / Henes, M. / Kosovrasti, K. / Nalivaika, E.A. / Ali, A. / KurtYilmaz, N. / Schiffer, C.A.
History
DepositionMar 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTLV-1 Protease
B: HTLV-1 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7093
Polymers25,1332
Non-polymers5761
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-23 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.897, 77.897, 160.081
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 9 or resid 11...
21(chain B and (resid 1 through 9 or resid 11...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROARGARG(chain A and (resid 1 through 9 or resid 11...AA1 - 91 - 9
12PROPROLEULEU(chain A and (resid 1 through 9 or resid 11...AA11 - 5111 - 51
13LYSLYSASNASN(chain A and (resid 1 through 9 or resid 11...AA52 - 5352 - 53
14PROPROPROPRO(chain A and (resid 1 through 9 or resid 11...AA1 - 1161 - 116
15PROPROPROPRO(chain A and (resid 1 through 9 or resid 11...AA1 - 1161 - 116
16PROPROPROPRO(chain A and (resid 1 through 9 or resid 11...AA1 - 1161 - 116
17PROPROPROPRO(chain A and (resid 1 through 9 or resid 11...AA1 - 1161 - 116
21PROPROARGARG(chain B and (resid 1 through 9 or resid 11...BB1 - 91 - 9
22PROPROLYSLYS(chain B and (resid 1 through 9 or resid 11...BB11 - 5211 - 52
23ASNASNASNASN(chain B and (resid 1 through 9 or resid 11...BB5353
24PROPROPROPRO(chain B and (resid 1 through 9 or resid 11...BB1 - 1161 - 116
25PROPROPROPRO(chain B and (resid 1 through 9 or resid 11...BB1 - 1161 - 116
26PROPROPROPRO(chain B and (resid 1 through 9 or resid 11...BB1 - 1161 - 116
27PROPROPROPRO(chain B and (resid 1 through 9 or resid 11...BB1 - 1161 - 116

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Components

#1: Protein HTLV-1 Protease


Mass: 12566.579 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-cell leukemia virus type I / Gene: pro / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y1C9N2
#2: Chemical ChemComp-A60 / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-3-{[(4-aminophenyl)sulfonyl](2-ethylbutyl)amino}-1-benzyl-2-hydroxypropyl]carbamate


Mass: 575.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C29H41N3O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 55.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 39-41% (v/v) PEG 300, 0.1M Phosphate/Citrate Buffer pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.07812 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 2.05→41.851 Å / Num. obs: 173500 / % possible obs: 99.79 % / Redundancy: 9.2 % / Biso Wilson estimate: 50.6 Å2 / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.03598 / Net I/σ(I): 12.24
Reflection shellResolution: 2.05→2.123 Å / Mean I/σ(I) obs: 0.74 / Num. unique obs: 15456 / CC1/2: 0.233 / CC star: 0.615 / Rpim(I) all: 1.253

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Aimlessdata scaling
PHASERphasing
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3wsj

3wsj


Resolution: 2.05→41.85 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.06
RfactorNum. reflection% reflection
Rfree0.2425 937 5 %
Rwork0.2205 --
obs0.2216 18742 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 191.64 Å2 / Biso mean: 71.4348 Å2 / Biso min: 35.15 Å2
Refinement stepCycle: final / Resolution: 2.05→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 81 36 1818
Biso mean--88.75 67.6 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121792
X-RAY DIFFRACTIONf_angle_d1.4122473
X-RAY DIFFRACTIONf_dihedral_angle_d11.3421261
X-RAY DIFFRACTIONf_chiral_restr0.073318
X-RAY DIFFRACTIONf_plane_restr0.009311
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A684X-RAY DIFFRACTION8.735TORSIONAL
12B684X-RAY DIFFRACTION8.735TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.0501-2.15820.41291280.39462450
2.1582-2.29340.40171310.31852492
2.2934-2.47050.27131300.26872480
2.4705-2.71910.29611330.2372508
2.7191-3.11240.26751330.23152537
3.1124-3.92080.26861360.21342575
3.9208-41.850.19281460.19362763

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