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- PDB-5dkp: Crystal Structure of N. meningitidis ClpP in complex with agonist... -

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Basic information

Entry
Database: PDB / ID: 5dkp
TitleCrystal Structure of N. meningitidis ClpP in complex with agonist ADEP A54556.
Components
  • ATP-dependent Clp protease proteolytic subunit
  • agonist ADEP A54556
Keywordshydrolase/antibiotic / Hydrolase / Agonist / Degradation / Antimicrobial / hydrolase-antibiotic complex
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / ATPase binding / serine-type endopeptidase activity / cytoplasm
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 speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.381 Å
AuthorsGoodreid, J.D. / Janetzko, J. / Santa Maria Jr., J.P. / Wong, K. / Leung, E. / Eger, B.T. / Bryson, S. / Pai, E.F. / Gray-Owen, S.D. / Walker, S. ...Goodreid, J.D. / Janetzko, J. / Santa Maria Jr., J.P. / Wong, K. / Leung, E. / Eger, B.T. / Bryson, S. / Pai, E.F. / Gray-Owen, S.D. / Walker, S. / Houry, W.A. / Batey, R.A.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)MOP-130374 Canada
CIHR Institute of Infection and ImmunityXNE-86945 Canada
CitationJournal: J.Med.Chem. / Year: 2016
Title: Development and Characterization of Potent Cyclic Acyldepsipeptide Analogues with Increased Antimicrobial Activity.
Authors: Goodreid, J.D. / Janetzko, J. / Santa Maria, J.P. / Wong, K.S. / Leung, E. / Eger, B.T. / Bryson, S. / Pai, E.F. / Gray-Owen, S.D. / Walker, S. / Houry, W.A. / Batey, R.A.
History
DepositionSep 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references / Structure summary
Revision 1.2Mar 30, 2016Group: Other
Revision 1.3Apr 6, 2016Group: Other
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.7Nov 15, 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

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
a: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease proteolytic subunit
c: ATP-dependent Clp protease proteolytic subunit
d: ATP-dependent Clp protease proteolytic subunit
e: ATP-dependent Clp protease proteolytic subunit
f: ATP-dependent Clp protease proteolytic subunit
g: ATP-dependent Clp protease proteolytic subunit
h: ATP-dependent Clp protease proteolytic subunit
i: ATP-dependent Clp protease proteolytic subunit
j: ATP-dependent Clp protease proteolytic subunit
k: ATP-dependent Clp protease proteolytic subunit
l: ATP-dependent Clp protease proteolytic subunit
m: ATP-dependent Clp protease proteolytic subunit
n: ATP-dependent Clp protease proteolytic subunit
O: agonist ADEP A54556
P: agonist ADEP A54556
Q: agonist ADEP A54556
R: agonist ADEP A54556
S: agonist ADEP A54556
T: agonist ADEP A54556
U: agonist ADEP A54556
V: agonist ADEP A54556
W: agonist ADEP A54556
X: agonist ADEP A54556
Y: agonist ADEP A54556
Z: agonist ADEP A54556
o: agonist ADEP A54556
p: agonist ADEP A54556
q: agonist ADEP A54556
r: agonist ADEP A54556
s: agonist ADEP A54556
t: agonist ADEP A54556
u: agonist ADEP A54556
v: agonist ADEP A54556
w: agonist ADEP A54556
x: agonist ADEP A54556
y: agonist ADEP A54556
z: agonist ADEP A54556
0: agonist ADEP A54556
1: agonist ADEP A54556
2: agonist ADEP A54556
3: agonist ADEP A54556
hetero molecules


Theoretical massNumber of molelcules
Total (without water)663,70087
Polymers662,53756
Non-polymers1,16431
Water15,385854
1
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
O: agonist ADEP A54556
P: agonist ADEP A54556
Q: agonist ADEP A54556
R: agonist ADEP A54556
S: agonist ADEP A54556
T: agonist ADEP A54556
U: agonist ADEP A54556
V: agonist ADEP A54556
W: agonist ADEP A54556
X: agonist ADEP A54556
Y: agonist ADEP A54556
Z: agonist ADEP A54556
o: agonist ADEP A54556
p: agonist ADEP A54556
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,81642
Polymers331,26828
Non-polymers54714
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
a: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease proteolytic subunit
c: ATP-dependent Clp protease proteolytic subunit
d: ATP-dependent Clp protease proteolytic subunit
e: ATP-dependent Clp protease proteolytic subunit
f: ATP-dependent Clp protease proteolytic subunit
g: ATP-dependent Clp protease proteolytic subunit
h: ATP-dependent Clp protease proteolytic subunit
i: ATP-dependent Clp protease proteolytic subunit
j: ATP-dependent Clp protease proteolytic subunit
k: ATP-dependent Clp protease proteolytic subunit
l: ATP-dependent Clp protease proteolytic subunit
m: ATP-dependent Clp protease proteolytic subunit
n: ATP-dependent Clp protease proteolytic subunit
q: agonist ADEP A54556
r: agonist ADEP A54556
s: agonist ADEP A54556
t: agonist ADEP A54556
u: agonist ADEP A54556
v: agonist ADEP A54556
w: agonist ADEP A54556
x: agonist ADEP A54556
y: agonist ADEP A54556
z: agonist ADEP A54556
0: agonist ADEP A54556
1: agonist ADEP A54556
2: agonist ADEP A54556
3: agonist ADEP A54556
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,88545
Polymers331,26828
Non-polymers61617
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.640, 198.850, 144.040
Angle α, β, γ (deg.)90.000, 97.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp


Mass: 22925.166 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Strain: MC58 / Gene: clpP, NMB1312 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JZ38, endopeptidase Clp
#2: Protein/peptide ...
agonist ADEP A54556


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 736.855 Da / Num. of mol.: 28 / Source method: obtained synthetically / References: NOR: NOR01131, ADEP1
#3: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM TRIS/HCl, pH 7.5, 200 mM KCl, 1 mM DTT, 10% glycerol

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→142.7 Å / Num. obs: 259622 / % possible obs: 99.6 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.173 / Net I/σ(I): 10.8
Reflection shellResolution: 2.39→2.59 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0G

4u0g


Resolution: 2.381→42.4 Å / FOM work R set: 0.8461 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.239 10324 3.98 %Random
Rwork0.1958 249298 --
obs0.1975 259622 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.23 Å2 / Biso mean: 26.58 Å2 / Biso min: 6.28 Å2
Refinement stepCycle: final / Resolution: 2.381→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41408 0 1487 854 43749
Biso mean--26.89 20.92 -
Num. residues----5328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00943571
X-RAY DIFFRACTIONf_angle_d1.28958727
X-RAY DIFFRACTIONf_chiral_restr0.0546591
X-RAY DIFFRACTIONf_plane_restr0.0067650
X-RAY DIFFRACTIONf_dihedral_angle_d14.02118481
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3814-2.40840.28113030.22397799810293
2.4084-2.43680.2783390.21828244858399
2.4368-2.46650.27463330.21488289862299
2.4665-2.49770.29513270.22398250857799
2.4977-2.53060.29333420.22788333867599
2.5306-2.56520.30573370.22058303864099
2.5652-2.60190.27723460.2118250859699
2.6019-2.64070.27573460.21488271861799
2.6407-2.6820.28183510.20728317866899
2.682-2.72590.26053480.20938323867199
2.7259-2.77290.26913360.21282578593100
2.7729-2.82330.26463380.209883548692100
2.8233-2.87760.27233420.210583218663100
2.8776-2.93640.24193380.202583318669100
2.9364-3.00020.25643460.200483138659100
3.0002-3.070.24593660.201682908656100
3.07-3.14670.25143500.211883048654100
3.1467-3.23180.26533590.211483008659100
3.2318-3.32680.24923550.206483308685100
3.3268-3.43410.26374020.209383038705100
3.4341-3.55680.25173670.201983158682100
3.5568-3.69920.22013360.192783708706100
3.6992-3.86740.22333420.188183138655100
3.8674-4.07120.2193450.174284008745100
4.0712-4.3260.19373750.167583358710100
4.326-4.65960.18543290.158983798708100
4.6596-5.12780.20193090.168184408749100
5.1278-5.86820.22933270.201184158742100
5.8682-7.38690.20593640.196284008764100
7.3869-42.40640.18463260.16858449877599

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