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- PDB-1zsz: Crystal structure of a computationally designed SspB heterodimer -

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Basic information

Entry
Database: PDB / ID: 1zsz
TitleCrystal structure of a computationally designed SspB heterodimer
Components(Stringent starvation protein B homolog) x 3
KeywordsDE NOVO PROTEIN / protein design / AAA / adaptor / specificity
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBolon, D.N. / Grant, R.A. / Baker, T.A. / Sauer, R.T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Specificity versus stability in computational protein design.
Authors: Bolon, D.N. / Grant, R.A. / Baker, T.A. / Sauer, R.T.
History
DepositionMay 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stringent starvation protein B homolog
B: Stringent starvation protein B homolog
C: Stringent starvation protein B homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9326
Polymers39,8593
Non-polymers733
Water1,67593
1
A: Stringent starvation protein B homolog
hetero molecules

A: Stringent starvation protein B homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0714
Polymers25,0222
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
B: Stringent starvation protein B homolog
C: Stringent starvation protein B homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3964
Polymers27,3482
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-17 kcal/mol
Surface area11320 Å2
MethodPISA
3
A: Stringent starvation protein B homolog
hetero molecules

A: Stringent starvation protein B homolog
hetero molecules

B: Stringent starvation protein B homolog
C: Stringent starvation protein B homolog
hetero molecules

B: Stringent starvation protein B homolog
C: Stringent starvation protein B homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,86312
Polymers79,7176
Non-polymers1466
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_556x+1/2,y+1/2,z+11
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area6550 Å2
ΔGint-70 kcal/mol
Surface area31690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.004, 61.036, 62.385
Angle α, β, γ (deg.)90.00, 110.87, 90.00
Int Tables number5
Space group name H-MC121
Detailschain b and c compose one biological unit, while chain A, forms a dimer across a crystal axis (to a crystallographically related chain A)

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Components

#1: Protein Stringent starvation protein B homolog


Mass: 12511.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: sspB / Plasmid: pET21, pACYCDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: P45206
#2: Protein Stringent starvation protein B homolog


Mass: 12578.135 Da / Num. of mol.: 1 / Mutation: A15S,Y16L,V101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: sspB / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: P45206
#3: Protein Stringent starvation protein B homolog


Mass: 14769.420 Da / Num. of mol.: 1 / Mutation: L12Y,A15G,Y16F,V101M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: sspB / Plasmid: pACYCDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: P45206
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: PEG 6000, CaCl2, sodium cacodylate, KCl, glycerol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2004
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 28612 / Num. obs: 28612 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.086
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.371 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ou9 chain A

1ou9


Resolution: 2→29.15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 432252.67 / Data cutoff high rms absF: 432252.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Chain A forms a dimer across a crystal axis and is an average of chains B and C. During refinement, residues which are different in chains B and C, were modeled with truncated side chains in ...Details: Chain A forms a dimer across a crystal axis and is an average of chains B and C. During refinement, residues which are different in chains B and C, were modeled with truncated side chains in chain A. The side chains for these residues are present in the chains B and C. The B/C dimer shows the asymmetric packing at the dimer interface that was introduced by computational design and was the focus of this study.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1348 4.8 %RANDOM
Rwork0.231 ---
all0.24 28612 --
obs0.242 27797 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.2607 Å2 / ksol: 0.352752 e/Å3
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.28 Å20 Å2-10.54 Å2
2--5.45 Å20 Å2
3----2.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 3 93 2646
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 202 4.6 %
Rwork0.288 4152 -
obs--91.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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