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- PDB-6mx2: Crystal Structure of ClpP1 from Clostridium difficile 630. -

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Basic information

Entry
Database: PDB / ID: 6mx2
TitleCrystal Structure of ClpP1 from Clostridium difficile 630.
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Casinolytic protease Tetradecamer Clostridium difficule
Function / homology
Function and homology information


endopeptidase Clp / ATP-dependent peptidase activity / 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
ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesClostridioides difficile 630 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsLavey, N.P. / Thomas, L.M. / Duerfeldt, A.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103640 United States
CitationJournal: To Be Published
Title: Crystal Structure of ClpP1 from Clostridium difficile 630.
Authors: Lavey, N.P. / Thomas, L.M. / Duerfeldt, A.S.
History
DepositionOct 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / struct
Item: _citation.title / _entity.src_method / _struct.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,03533
Polymers298,46014
Non-polymers57519
Water13,980776
1
A: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3422
Polymers21,3191
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3422
Polymers21,3191
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3422
Polymers21,3191
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3422
Polymers21,3191
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3422
Polymers21,3191
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3422
Polymers21,3191
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3653
Polymers21,3191
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3422
Polymers21,3191
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3653
Polymers21,3191
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3422
Polymers21,3191
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3422
Polymers21,3191
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3653
Polymers21,3191
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4343
Polymers21,3191
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4343
Polymers21,3191
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.328, 97.372, 106.494
Angle α, β, γ (deg.)113.150, 104.560, 103.210
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 21318.598 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile 630 (bacteria)
Strain: 630 / Gene: clpP1, clpP, CD630_33050 / Production host: Escherichia coli (E. coli) / Strain (production host): JK10 / References: UniProt: Q180F0, endopeptidase Clp
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 776 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 2.4 M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.12 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. obs: 109969 / % possible obs: 98.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.118 / Rrim(I) all: 0.248 / Χ2: 1.11 / Net I/σ(I): 3.3 / Num. measured all: 460705
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.544.30.58253560.7260.3110.6620.21396.6
2.54-2.594.40.5453940.7280.2860.6120.22396.8
2.59-2.644.30.50254700.7660.2660.5690.26797.1
2.64-2.694.30.49554490.7530.2630.5620.32697.5
2.69-2.754.10.42654770.8080.2280.4850.32798.3
2.75-2.824.40.455440.8210.210.4520.37698.9
2.82-2.894.50.36855890.8350.1920.4160.49399.3
2.89-2.964.50.32355850.8760.1680.3650.59599.8
2.96-3.054.40.30855650.8760.1610.3480.71199.8
3.05-3.154.40.28155550.8850.1480.3180.93699.8
3.15-3.264.30.25855350.9120.1360.2921.05299
3.26-3.393.90.22255170.9140.1230.2541.17398.3
3.39-3.553.70.254840.9170.1160.2321.3398.1
3.55-3.733.40.15953410.7770.0990.1881.34395.8
3.73-3.973.30.14453280.7940.0890.171.31395.5
3.97-4.2740.16455130.9520.090.1872.05798.3
4.27-4.74.40.16855720.9570.0880.192.93199.5
4.7-5.384.50.17155920.9640.0890.1932.1999.8
5.38-6.774.30.18255340.950.0960.2061.81699.1
6.77-354.30.1455690.9730.0740.1592.63799.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.27 Å34.9 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QWD

3qwd


Resolution: 2.5→34.898 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.93
RfactorNum. reflection% reflection
Rfree0.2441 5435 4.94 %
Rwork0.1929 --
obs0.1954 109927 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.38 Å2 / Biso mean: 30.4022 Å2 / Biso min: 11.4 Å2
Refinement stepCycle: final / Resolution: 2.5→34.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19627 0 29 776 20432
Biso mean--30.44 30.26 -
Num. residues----2551
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4978-2.52620.32561600.23323056321688
2.5262-2.55590.30021940.2273490368497
2.5559-2.5870.31311670.23483406357397
2.587-2.61980.29111700.2313484365497
2.6198-2.65420.30991670.22773449361697
2.6542-2.69060.30971500.23763506365698
2.6906-2.7290.31092040.22853477368198
2.729-2.76970.30511710.23213508367999
2.7697-2.8130.33662010.23283497369899
2.813-2.85910.30761850.23163537372299
2.8591-2.90840.29251700.217834853655100
2.9084-2.96120.28371790.207436133792100
2.9612-3.01810.26491810.217835263707100
3.0181-3.07970.29292020.22835193721100
3.0797-3.14660.30482020.223835493751100
3.1466-3.21980.23231990.20713540373999
3.2198-3.30030.26591630.20793499366298
3.3003-3.38940.27131680.20213511367998
3.3894-3.48910.24511960.19333483367998
3.4891-3.60160.2291820.18473467364997
3.6016-3.73020.22521630.18253374353795
3.7302-3.87930.23541830.18383421360495
3.8793-4.05560.20941930.16793416360997
4.0556-4.26910.20531810.15853484366599
4.2691-4.5360.19172060.15053471367799
4.536-4.88540.21281800.150136043784100
4.8854-5.37540.2081750.178935593734100
5.3754-6.14960.2631690.207135553724100
6.1496-7.73390.20992050.18073486369199
7.7339-34.90170.13751690.15643520368998

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