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- PDB-3mt6: Structure of ClpP from Escherichia coli in complex with ADEP1 -

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Basic information

Entry
Database: PDB / ID: 3mt6
TitleStructure of ClpP from Escherichia coli in complex with ADEP1
Components
  • ACYLDEPSIPEPTIDE 1
  • ATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE/ANTIBIOTIC / ENDOPEPTIDASE CLP / CASEINOLYTIC PROTEASE / PROTEASE TI / ACYPDEPSIPEPTIDE ANTIBIOTICS / HYDROLASE-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


HslUV protease complex / endopeptidase Clp complex / endopeptidase Clp / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / serine-type peptidase activity / proteasomal protein catabolic process / response to radiation ...HslUV protease complex / endopeptidase Clp complex / endopeptidase Clp / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / serine-type peptidase activity / proteasomal protein catabolic process / response to radiation / ATPase binding / response to heat / serine-type endopeptidase activity / proteolysis / membrane / identical protein binding / cytosol
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADEP1 / : / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
STREPTOMYCES HAWAIIENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsChung, Y.S.
CitationJournal: Chem.Biol. / Year: 2010
Title: Acyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: A model for the ClpX/ClpA-bound state of ClpP.
Authors: Li, D.H. / Chung, Y.S. / Gloyd, M. / Joseph, E. / Ghirlando, R. / Wright, G.D. / Cheng, Y.Q. / Maurizi, M.R. / Guarne, A. / Ortega, J.
History
DepositionApr 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Mar 30, 2016Group: Non-polymer description
Revision 1.4Sep 6, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: ATP-dependent Clp protease proteolytic subunit
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
U: ATP-dependent Clp protease proteolytic subunit
O: ATP-dependent Clp protease proteolytic subunit
P: ATP-dependent Clp protease proteolytic subunit
Q: ATP-dependent Clp protease proteolytic subunit
Y: ATP-dependent Clp protease proteolytic subunit
Z: ATP-dependent Clp protease proteolytic subunit
a: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease proteolytic subunit
V: ATP-dependent Clp protease proteolytic subunit
W: ATP-dependent Clp protease proteolytic subunit
X: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
A: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
1: ACYLDEPSIPEPTIDE 1
2: ACYLDEPSIPEPTIDE 1
c: ACYLDEPSIPEPTIDE 1
d: ACYLDEPSIPEPTIDE 1
e: ACYLDEPSIPEPTIDE 1
f: ACYLDEPSIPEPTIDE 1
g: ACYLDEPSIPEPTIDE 1
h: ACYLDEPSIPEPTIDE 1
i: ACYLDEPSIPEPTIDE 1
j: ACYLDEPSIPEPTIDE 1
k: ACYLDEPSIPEPTIDE 1
l: ACYLDEPSIPEPTIDE 1
m: ACYLDEPSIPEPTIDE 1
n: ACYLDEPSIPEPTIDE 1
o: ACYLDEPSIPEPTIDE 1
p: ACYLDEPSIPEPTIDE 1
q: ACYLDEPSIPEPTIDE 1
r: ACYLDEPSIPEPTIDE 1
s: ACYLDEPSIPEPTIDE 1
t: ACYLDEPSIPEPTIDE 1
v: ACYLDEPSIPEPTIDE 1
w: ACYLDEPSIPEPTIDE 1
x: ACYLDEPSIPEPTIDE 1
y: ACYLDEPSIPEPTIDE 1
z: ACYLDEPSIPEPTIDE 1
3: ACYLDEPSIPEPTIDE 1
4: ACYLDEPSIPEPTIDE 1
u: ACYLDEPSIPEPTIDE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)677,086111
Polymers670,58656
Non-polymers6,50055
Water64,6923591
1
R: ATP-dependent Clp protease proteolytic subunit
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
U: ATP-dependent Clp protease proteolytic subunit
O: ATP-dependent Clp protease proteolytic subunit
P: ATP-dependent Clp protease proteolytic subunit
Q: ATP-dependent Clp protease proteolytic subunit
Y: ATP-dependent Clp protease proteolytic subunit
Z: ATP-dependent Clp protease proteolytic subunit
a: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease proteolytic subunit
V: ATP-dependent Clp protease proteolytic subunit
W: ATP-dependent Clp protease proteolytic subunit
X: ATP-dependent Clp protease proteolytic subunit
o: ACYLDEPSIPEPTIDE 1
p: ACYLDEPSIPEPTIDE 1
q: ACYLDEPSIPEPTIDE 1
r: ACYLDEPSIPEPTIDE 1
s: ACYLDEPSIPEPTIDE 1
t: ACYLDEPSIPEPTIDE 1
v: ACYLDEPSIPEPTIDE 1
w: ACYLDEPSIPEPTIDE 1
x: ACYLDEPSIPEPTIDE 1
y: ACYLDEPSIPEPTIDE 1
z: ACYLDEPSIPEPTIDE 1
3: ACYLDEPSIPEPTIDE 1
4: ACYLDEPSIPEPTIDE 1
u: ACYLDEPSIPEPTIDE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,48455
Polymers335,29328
Non-polymers3,19127
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area67900 Å2
ΔGint-377 kcal/mol
Surface area91800 Å2
MethodPISA
2
M: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
A: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
1: ACYLDEPSIPEPTIDE 1
2: ACYLDEPSIPEPTIDE 1
c: ACYLDEPSIPEPTIDE 1
d: ACYLDEPSIPEPTIDE 1
e: ACYLDEPSIPEPTIDE 1
f: ACYLDEPSIPEPTIDE 1
g: ACYLDEPSIPEPTIDE 1
h: ACYLDEPSIPEPTIDE 1
i: ACYLDEPSIPEPTIDE 1
j: ACYLDEPSIPEPTIDE 1
k: ACYLDEPSIPEPTIDE 1
l: ACYLDEPSIPEPTIDE 1
m: ACYLDEPSIPEPTIDE 1
n: ACYLDEPSIPEPTIDE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,60256
Polymers335,29328
Non-polymers3,30928
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area69790 Å2
ΔGint-375 kcal/mol
Surface area94440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.254, 121.150, 276.170
Angle α, β, γ (deg.)90.00, 91.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
ATP-dependent Clp protease proteolytic subunit / / ADEP1 / Endopeptidase Clp / Caseinolytic protease / Protease Ti / Heat shock protein F21.5


Mass: 23212.650 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0437, clpP, JW0427, lopP / Plasmid: PET9A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6G7, endopeptidase Clp
#2: Protein/peptide ...
ACYLDEPSIPEPTIDE 1


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 736.855 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Source: (natural) STREPTOMYCES HAWAIIENSIS (bacteria) / Genus: CLPP, YVDN, BSU34540 / References: NOR: NOR01131, ADEP1
#3: Chemical...
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3591 / 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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25-35% (v/v) MPD and 0.1 M sodium acetate at pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2010 / Details: Mirror
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 472053 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.065 / Rsym value: 0.058 / Net I/σ(I): 11.7

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.4_159)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YG6

1yg6


Resolution: 1.901→29.902 Å / SU ML: 0.22 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 5212 1.1 %
Rwork0.1781 --
obs0.1784 471961 98.14 %
all-477173 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.508 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.8565 Å2-0 Å2-3.3535 Å2
2---0.4994 Å2-0 Å2
3----0.357 Å2
Refinement stepCycle: LAST / Resolution: 1.901→29.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42241 0 440 3591 46272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343582
X-RAY DIFFRACTIONf_angle_d0.84658876
X-RAY DIFFRACTIONf_dihedral_angle_d19.41417232
X-RAY DIFFRACTIONf_chiral_restr0.066653
X-RAY DIFFRACTIONf_plane_restr0.0077514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-1.96890.27654280.223940947X-RAY DIFFRACTION86
1.9689-2.04770.25125300.209846245X-RAY DIFFRACTION98
2.0477-2.14090.23164630.195546983X-RAY DIFFRACTION99
2.1409-2.25370.22565760.191247053X-RAY DIFFRACTION99
2.2537-2.39490.22815440.185747325X-RAY DIFFRACTION100
2.3949-2.57970.21445380.188447350X-RAY DIFFRACTION100
2.5797-2.83910.21485330.186347451X-RAY DIFFRACTION100
2.8391-3.24950.19995350.1847571X-RAY DIFFRACTION100
3.2495-4.09240.18485250.160847682X-RAY DIFFRACTION100
4.0924-29.90530.16715400.15648142X-RAY DIFFRACTION100

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