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- PDB-4yjx: The structure of Agrobacterium tumefaciens ClpS2 bound to L-pheny... -

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Basic information

Entry
Database: PDB / ID: 4yjx
TitleThe structure of Agrobacterium tumefaciens ClpS2 bound to L-phenylalaninamide
ComponentsATP-dependent Clp protease adapter protein ClpS 2
KeywordsPROTEIN BINDING / N-end rule / Protease adaptor
Function / homology
Function and homology information


protein catabolic process / proteolysis
Similarity search - Function
Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS / ATP-dependent Clp protease adaptor protein ClpS / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Ribosomal Protein L30; Chain: A, / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHENYLALANINE AMIDE / ATP-dependent Clp protease adapter protein ClpS 2
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.547 Å
AuthorsStein, B. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049224 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Structure / Year: 2016
Title: Structural Basis of an N-Degron Adaptor with More Stringent Specificity.
Authors: Stein, B.J. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Dec 28, 2016Group: Structure summary
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease adapter protein ClpS 2
B: ATP-dependent Clp protease adapter protein ClpS 2
C: ATP-dependent Clp protease adapter protein ClpS 2
D: ATP-dependent Clp protease adapter protein ClpS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,78011
Polymers46,8354
Non-polymers9457
Water1,13563
1
A: ATP-dependent Clp protease adapter protein ClpS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9693
Polymers11,7091
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-dependent Clp protease adapter protein ClpS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8732
Polymers11,7091
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ATP-dependent Clp protease adapter protein ClpS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0654
Polymers11,7091
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ATP-dependent Clp protease adapter protein ClpS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8732
Polymers11,7091
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.033, 92.997, 94.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ATP-dependent Clp protease adapter protein ClpS 2


Mass: 11708.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / Gene: clpS2, Atu2232, AGR_C_4060 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: Q8UD95
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NFA / PHENYLALANINE AMIDE


Type: L-peptide linking / Mass: 164.204 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12N2O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 2.2M Ammonium Sulfate 0.2M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.547→33.864 Å / Num. obs: 17257 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 36.44 Å2 / Rsym value: 0.098 / Net I/σ(I): 19.5
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.08 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YJM

4yjm


Resolution: 2.547→33.864 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 819 4.75 %
Rwork0.1753 --
obs0.1771 17257 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.547→33.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 63 63 2771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042749
X-RAY DIFFRACTIONf_angle_d0.8133698
X-RAY DIFFRACTIONf_dihedral_angle_d11.5111036
X-RAY DIFFRACTIONf_chiral_restr0.028421
X-RAY DIFFRACTIONf_plane_restr0.003470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5468-2.70630.22381330.21132685X-RAY DIFFRACTION100
2.7063-2.91510.30561560.20632669X-RAY DIFFRACTION100
2.9151-3.20830.22911600.19792680X-RAY DIFFRACTION100
3.2083-3.6720.22951220.17892739X-RAY DIFFRACTION100
3.672-4.62450.17131260.14172760X-RAY DIFFRACTION100
4.6245-33.86740.19861220.1752905X-RAY DIFFRACTION100
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)
12.814-0.5077-0.43494.93310.1382.51070.0055-0.0916-0.0374-0.20080.0110.23020.0964-0.1895-0.00720.233-0.02470.01360.29370.02630.2175-20.677311.79010.1429
23.3270.91680.1443.32822.21824.1023-0.0139-0.05020.00270.15370.1223-0.19120.12960.2947-0.10580.18860.0144-0.00060.22380.01220.2349-3.157216.6566-8.8259
33.2049-0.50240.53584.70090.08943.7886-0.0787-0.1516-0.04960.18710.13530.00390.0905-0.0865-0.03120.27860.0051-0.00270.244-0.0430.2482-7.9417-2.0775-26.7789
43.9282.1464-0.21115.870.14274.0256-0.11150.40330.2693-0.69870.17230.1409-0.18770.059-0.05760.3855-0.0135-0.01130.28730.00110.2473-2.924926.0443-28.959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B
3X-RAY DIFFRACTION3Chain C
4X-RAY DIFFRACTION4Chain D

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