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- PDB-1ou8: structure of an AAA+ protease delivery protein in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 1ou8
Titlestructure of an AAA+ protease delivery protein in complex with a peptide degradation tag
Components
  • Stringent starvation protein B homolog
  • synthetic ssrA peptide
KeywordsTRANSPORT PROTEIN / peptide-binding pocket / protein-peptide complex / homodimer
Function / homology
Function and homology information


positive regulation of protein catabolic process / ribosome / cytosol
Similarity search - Function
SspB-like / Stringent starvation protein B / SspB-like superfamily / Stringent starvation protein B / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Stringent starvation protein B homolog
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLevchenko, I. / Grant, R.A. / Wah, D.A. / Sauer, R.T. / Baker, T.A.
Citation
Journal: Mol.Cell / Year: 2003
Title: Structure of a delivery protein for an AAA+ protease in complex with a peptide degradation tag
Authors: Levchenko, I. / Grant, R.A. / Wah, D.A. / Sauer, R.T. / Baker, T.A.
#1: Journal: Science / Year: 2000
Title: a specificity-enhancing factor for the ClpXP degradation machine
Authors: Levchenko, I. / Siedel, M. / Sauer, R.T. / Baker, T.A.
History
DepositionMar 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_struct_assembly ...pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.4Aug 16, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _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: Stringent starvation protein B homolog
B: Stringent starvation protein B homolog
C: synthetic ssrA peptide
D: synthetic ssrA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7396
Polymers27,6914
Non-polymers492
Water3,279182
1
A: Stringent starvation protein B homolog
C: synthetic ssrA peptide
hetero molecules

A: Stringent starvation protein B homolog
C: synthetic ssrA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7396
Polymers27,6914
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
Buried area3910 Å2
ΔGint-24 kcal/mol
Surface area12050 Å2
MethodPISA
2
B: Stringent starvation protein B homolog
D: synthetic ssrA peptide
hetero molecules

B: Stringent starvation protein B homolog
D: synthetic ssrA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7396
Polymers27,6914
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3620 Å2
ΔGint-27 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.020, 69.020, 104.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Stringent starvation protein B homolog


Mass: 12640.204 Da / Num. of mol.: 2 / Fragment: residues 1-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: SSPB / Production host: Escherichia coli (E. coli) / References: UniProt: P45206
#2: Protein/peptide synthetic ssrA peptide


Mass: 1205.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.55 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: sodium citrate, sodium cacodylate, sodium thiocyanate, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.7 mg/mlprotein1drop
20.24 Mcalcium acetate1reservoir
30.1 Msodium cacodylate1reservoirpH5.6
412 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.92108 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 30, 2002
RadiationMonochromator: KOHZU double crystal monochromator sagitally focused second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92108 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 38849 / Num. obs: 38849 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 17.8 Å2 / Rsym value: 0.107
Reflection shellResolution: 1.6→1.7 Å / Rsym value: 0.634 / % possible all: 100
Reflection
*PLUS
Num. measured all: 418776 / Rmerge(I) obs: 0.107
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OU9

1ou9


Resolution: 1.6→14.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 226623.29 / Data cutoff high rms absF: 226623.29 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3770 10 %RANDOM
Rwork0.206 ---
all0.21 38849 --
obs0.21 37665 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.8539 Å2 / ksol: 0.411845 e/Å3
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.61 Å20 Å2
2--0.61 Å20 Å2
3----1.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.6→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 2 182 2019
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 586 9.9 %
Rwork0.224 5357 -
obs--93.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Version: 1.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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