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- PDB-4yjm: The apo structure of Agrobacterium tumefaciens ClpS2 -

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Basic information

Entry
Database: PDB / ID: 4yjm
TitleThe apo structure of Agrobacterium tumefaciens ClpS2
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
ATP-dependent Clp protease adapter protein ClpS 2
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.952 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 / Other
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


Theoretical massNumber of molelcules
Total (without water)46,8354
Polymers46,8354
Non-polymers00
Water3,873215
1
A: ATP-dependent Clp protease adapter protein ClpS 2


Theoretical massNumber of molelcules
Total (without water)11,7091
Polymers11,7091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent Clp protease adapter protein ClpS 2


Theoretical massNumber of molelcules
Total (without water)11,7091
Polymers11,7091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ATP-dependent Clp protease adapter protein ClpS 2


Theoretical massNumber of molelcules
Total (without water)11,7091
Polymers11,7091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ATP-dependent Clp protease adapter protein ClpS 2


Theoretical massNumber of molelcules
Total (without water)11,7091
Polymers11,7091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: ATP-dependent Clp protease adapter protein ClpS 2
D: ATP-dependent Clp protease adapter protein ClpS 2

C: ATP-dependent Clp protease adapter protein ClpS 2

A: ATP-dependent Clp protease adapter protein ClpS 2


Theoretical massNumber of molelcules
Total (without water)46,8354
Polymers46,8354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area6030 Å2
ΔGint-39 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.007, 92.550, 96.464
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 tumefaciens (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.76 Å3/Da / Density % sol: 55.5 %
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: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.952→18.543 Å / Num. obs: 38281 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rsym value: 0.067 / Net I/σ(I): 34.74

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DNJ

3dnj


Resolution: 1.952→18.543 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 1862 4.86 %Random Selection
Rwork0.1774 ---
obs0.1789 36420 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.952→18.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 0 215 2886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122715
X-RAY DIFFRACTIONf_angle_d1.1763655
X-RAY DIFFRACTIONf_dihedral_angle_d10.9021043
X-RAY DIFFRACTIONf_chiral_restr0.052421
X-RAY DIFFRACTIONf_plane_restr0.006467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9522-2.0050.20461170.21152699X-RAY DIFFRACTION97
2.005-2.06390.24161510.20762761X-RAY DIFFRACTION100
2.0639-2.13040.25171520.19492759X-RAY DIFFRACTION100
2.1304-2.20640.25091670.18832747X-RAY DIFFRACTION100
2.2064-2.29460.20981210.17872794X-RAY DIFFRACTION100
2.2946-2.39890.19981470.16782789X-RAY DIFFRACTION100
2.3989-2.5250.19611450.17672781X-RAY DIFFRACTION100
2.525-2.68280.22171440.18982796X-RAY DIFFRACTION100
2.6828-2.88920.22941620.18492791X-RAY DIFFRACTION100
2.8892-3.17870.22871610.19352784X-RAY DIFFRACTION100
3.1787-3.63560.20841390.17562857X-RAY DIFFRACTION100
3.6356-4.56920.1531310.15022873X-RAY DIFFRACTION100
4.5692-18.54410.2211250.18022989X-RAY DIFFRACTION99
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
13.0826-0.258-1.1047.9105-1.58084.5846-0.0077-0.0099-0.1946-0.5445-0.19350.19580.4229-0.00720.18210.16580.01440.01820.28660.02320.2107Chain A-21.18412.7641-0.1009
22.74090.85830.09894.50863.02244.5367-0.0344-0.0195-0.14220.14440.1122-0.14670.29590.3373-0.03510.12630.03120.00480.20270.02910.1981Chain B-3.56416.147-8.2988
33.3749-1.19421.49845.22661.07255.0885-0.1347-0.21-0.00650.3640.08670.12390.2428-0.1440.0440.2708-0.0034-0.0050.1909-0.06750.2427Chain C-8.1424-2.1-27.4739
42.03051.0331-0.55934.7312-0.21262.608-0.22590.34520.3412-1.27760.21310.1483-0.38980.02720.00030.6186-0.0887-0.03580.31170.01970.2583Chain D-2.317826.002-29.7375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain AA18 - 102
2X-RAY DIFFRACTION2Chain BB20 - 103
3X-RAY DIFFRACTION3Chain CC20 - 102
4X-RAY DIFFRACTION4Chain DD19 - 102

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