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- PDB-2wa9: Structural basis of N-end rule substrate recognition in Escherich... -

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Basic information

Entry
Database: PDB / ID: 2wa9
TitleStructural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS - Trp peptide structure
Components
  • ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
  • TRP PEPTIDE
KeywordsPEPTIDE BINDING PROTEIN / CLPS / CLPA / CLPP / N-END RULE RECOGNITION / PEPTIDE-BINDING PROTEIN
Function / homology
Function and homology information


molecular function inhibitor activity / protein catabolic process / response to heat / protein-folding chaperone binding / 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
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSchuenemann, V.J. / Kralik, S.M. / Albrecht, R. / Spall, S.K. / Truscott, K.N. / Dougan, D.A. / Zeth, K.
CitationJournal: Embo Rep. / Year: 2009
Title: Structural Basis of N-End Rule Substrate Recognition in Escherichia Coli by the Clpap Adaptor Protein Clps.
Authors: Schuenemann, V.J. / Kralik, S.M. / Albrecht, R. / Spall, S.K. / Truscott, K.N. / Dougan, D.A. / Zeth, K.
History
DepositionFeb 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 16, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
B: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
C: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
D: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
E: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
F: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
G: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
H: TRP PEPTIDE
I: TRP PEPTIDE
J: TRP PEPTIDE
K: TRP PEPTIDE
L: TRP PEPTIDE
M: TRP PEPTIDE
N: TRP PEPTIDE


Theoretical massNumber of molelcules
Total (without water)88,66614
Polymers88,66614
Non-polymers00
Water0
1
A: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
H: TRP PEPTIDE


Theoretical massNumber of molelcules
Total (without water)12,6672
Polymers12,6672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
I: TRP PEPTIDE


Theoretical massNumber of molelcules
Total (without water)12,6672
Polymers12,6672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
J: TRP PEPTIDE


Theoretical massNumber of molelcules
Total (without water)12,6672
Polymers12,6672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
K: TRP PEPTIDE


Theoretical massNumber of molelcules
Total (without water)12,6672
Polymers12,6672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
L: TRP PEPTIDE


Theoretical massNumber of molelcules
Total (without water)12,6672
Polymers12,6672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
M: TRP PEPTIDE


Theoretical massNumber of molelcules
Total (without water)12,6672
Polymers12,6672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
N: TRP PEPTIDE


Theoretical massNumber of molelcules
Total (without water)12,6672
Polymers12,6672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)171.910, 155.870, 71.230
Angle α, β, γ (deg.)90.00, 114.64, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A25 - 103
2113B25 - 103
3113C25 - 103
4113D25 - 103
5113E25 - 103
6113F25 - 103
7113G25 - 103

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Components

#1: Protein
ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS / CLPS - PHE-PEPTIDE COMPLEX


Mass: 12321.168 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(GOLD) / References: UniProt: P0A8Q6
#2: Protein/peptide
TRP PEPTIDE


Mass: 345.435 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)

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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: 2.6 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.294
11H+2.000L, -K, -L20.289
11-K+L, -H-L, -L30.19
11K+L, H+L, -L40.228
ReflectionResolution: 2.9→30 Å / Num. obs: 19203 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 11
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0063refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→25 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.897 / SU B: 23.578 / SU ML: 0.262 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1890 5 %RANDOM
Rwork0.236 ---
obs0.237 19203 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.08 Å2
Baniso -1Baniso -2Baniso -3
1-14.71 Å20 Å214.57 Å2
2---14.08 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4880 0 0 0 4880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224969
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9756721
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9535602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27525210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.04615887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2311514
X-RAY DIFFRACTIONr_chiral_restr0.1020.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213614
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5031.53072
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95824973
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2231897
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7744.51748
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A312tight positional0.050.05
2B312tight positional0.050.05
3C312tight positional0.050.05
4D312tight positional0.050.05
5E312tight positional0.050.05
6F312tight positional0.050.05
7G312tight positional0.060.05
1A314loose positional0.065
2B314loose positional0.065
3C314loose positional0.065
4D314loose positional0.065
5E314loose positional0.055
6F314loose positional0.065
7G314loose positional0.075
1A312tight thermal0.120.5
2B312tight thermal0.110.5
3C312tight thermal0.110.5
4D312tight thermal0.120.5
5E312tight thermal0.090.5
6F312tight thermal0.140.5
7G312tight thermal0.140.5
1A314loose thermal0.1210
2B314loose thermal0.110
3C314loose thermal0.1210
4D314loose thermal0.1210
5E314loose thermal0.1110
6F314loose thermal0.1410
7G314loose thermal0.1210
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 103
Rwork0.261 2609
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)
14.2266-2.29660.42482.3066-0.69343.37380.259-0.22880.14570.1852-0.00670.0349-0.46330.3206-0.25220.2636-0.04430.02450.0716-0.05620.055449.457-2.13413.642
21.8371-1.69130.29354.79570.15843.97590.35050.38570.0742-0.1696-0.18270.17440.3328-0.5354-0.16770.25010.00660.00540.20340.04860.065143.813-12.048-6.609
33.862-1.4547-0.31863.63020.49854.54250.2692-0.11410.0496-0.1831-0.0908-0.04750.3254-0.3718-0.17830.2957-0.01960.09150.06670.04350.070343.1752.7-28.265
46.8106-2.935-0.40163.8119-0.51494.25150.0101-0.24750.42150.07290.1976-0.2387-0.2140.3638-0.20770.15290.00550.05790.0633-0.00610.091532.60412.64627.411
56.4109-3.8178-1.03019.78350.88282.5620.22640.6595-0.5805-0.18810.0535-0.0363-0.05490.0989-0.27980.8587-0.07540.11130.3552-0.07460.960159.949-27.422-22.516
60.84220.4643-0.20759.0256-1.52742.3909-0.11830.2403-0.008-0.7282-0.0194-0.12050.22520.50930.13770.3676-0.02450.05930.21410.0340.103932.70728.6355.848
79.3127.35121.73312.94690.86822.5268-0.175-0.34831.28110.22410.0911.93530.2293-0.59810.0840.35040.04320.09750.2776-0.02250.54218.7359.866-18.714
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 100
2X-RAY DIFFRACTION2B30 - 100
3X-RAY DIFFRACTION3C30 - 100
4X-RAY DIFFRACTION4D30 - 100
5X-RAY DIFFRACTION5E30 - 100
6X-RAY DIFFRACTION6F30 - 100
7X-RAY DIFFRACTION7G30 - 100

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