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- PDB-3q7h: Structure of the ClpP subunit of the ATP-dependent Clp Protease f... -

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Basic information

Entry
Database: PDB / ID: 3q7h
TitleStructure of the ClpP subunit of the ATP-dependent Clp Protease from Coxiella burnetii
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / alpha and beta protein / ClpP/crotonase fold
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine 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
DI(HYDROXYETHYL)ETHER / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Gordon, E. / Hasseman, J. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Structure of the ClpP subunit of the ATP-dependent Clp Protease from Coxiella burnetii
Authors: Anderson, S.M. / Wawrzak, Z. / Gordon, E. / Hasseman, J. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)312,00875
Polymers307,38414
Non-polymers4,62461
Water24,4101355
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.912, 137.469, 127.784
Angle α, β, γ (deg.)90.0, 109.03, 90.0
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21M
12B
22C
32D
42G
52H
62I
13K
23N
14A
24E
34F
44J

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUPROPROchain L and (resseq 4:195 )LL4 - 1954 - 195
211LEULEUPROPROchain M and (resseq 4:195 )MM4 - 1954 - 195
112VALVALGLUGLUchain B and (resseq 5:10 or resseq 17:192 )BB5 - 105 - 10
122ARGARGLYSLYSchain B and (resseq 5:10 or resseq 17:192 )BB17 - 19217 - 192
212VALVALGLUGLUchain C and (resseq 5:10 or resseq 17:192 )CC5 - 105 - 10
222ARGARGLYSLYSchain C and (resseq 5:10 or resseq 17:192 )CC17 - 19217 - 192
312VALVALGLUGLUchain D and (resseq 5:10 or resseq 17:192 )DD5 - 105 - 10
322ARGARGLYSLYSchain D and (resseq 5:10 or resseq 17:192 )DD17 - 19217 - 192
412VALVALGLUGLUchain G and (resseq 5:10 or resseq 17:192 )GG5 - 105 - 10
422ARGARGLYSLYSchain G and (resseq 5:10 or resseq 17:192 )GG17 - 19217 - 192
512VALVALGLUGLUchain H and (resseq 5:10 or resseq 17:192 )HH5 - 105 - 10
522ARGARGLYSLYSchain H and (resseq 5:10 or resseq 17:192 )HH17 - 19217 - 192
612VALVALGLUGLUchain I and (resseq 5:10 or resseq 17:192 )II5 - 105 - 10
622ARGARGLYSLYSchain I and (resseq 5:10 or resseq 17:192 )II17 - 19217 - 192
113LEULEUTHRTHRchain K and (resseq 4:12 or resseq 17:192 )KK4 - 124 - 12
123ARGARGLYSLYSchain K and (resseq 4:12 or resseq 17:192 )KK17 - 19217 - 192
213LEULEUTHRTHRchain N and (resseq 4:12 or resseq 17:192 )NN4 - 124 - 12
223ARGARGLYSLYSchain N and (resseq 4:12 or resseq 17:192 )NN17 - 19217 - 192
114LEULEUGLUGLUchain A and (resseq 4:10 or resseq 19:195 )AA4 - 104 - 10
124TYRTYRPROPROchain A and (resseq 4:10 or resseq 19:195 )AA19 - 19519 - 195
214LEULEUGLUGLUchain E and (resseq 4:10 or resseq 19:195 )EE4 - 104 - 10
224TYRTYRPROPROchain E and (resseq 4:10 or resseq 19:195 )EE19 - 19519 - 195
314LEULEUGLUGLUchain F and (resseq 4:10 or resseq 19:195 )FF4 - 104 - 10
324TYRTYRPROPROchain F and (resseq 4:10 or resseq 19:195 )FF19 - 19519 - 195
414LEULEUGLUGLUchain J and (resseq 4:10 or resseq 19:195 )JJ4 - 104 - 10
424TYRTYRPROPROchain J and (resseq 4:10 or resseq 19:195 )JJ19 - 19519 - 195

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.609275, -0.014988, -0.792817), (-0.022154, -0.999753, 0.001874), (-0.792649, 0.016422, -0.609456)30.0158, 0.592188, 60.7728
2given(-0.435288, 0.680525, 0.589415), (0.682422, -0.177619, 0.709049), (0.587217, 0.710871, -0.38709)12.4477, -33.520901, 27.240299
3given(0.64725, -0.553563, -0.524057), (0.394195, 0.831492, -0.391448), (0.65244, 0.046784, 0.756395)22.0637, 3.02459, -6.13841
4given(0.825292, 0.528971, -0.197694), (0.527581, -0.847082, -0.064112), (-0.201376, -0.051389, -0.978165)9.31464, -8.92871, 59.316399
5given(-0.747705, -0.663927, -0.011782), (-0.142942, 0.178257, -0.973546), (0.648464, -0.726241, -0.228187)35.287998, 29.8731, 21.138
6given(0.608997, -0.020302, -0.792913), (-0.021688, -0.999725, 0.00894), (-0.792876, 0.011752, -0.60927)29.990299, 0.138109, 60.7612
7given(0.604723, -0.020208, -0.796179), (-0.019528, -0.999754, 0.010542), (-0.796196, 0.009173, -0.604969)29.878201, 0.109739, 60.6744
8given(-0.119719, -0.839167, -0.530533), (0.320111, 0.47321, -0.820732), (0.939785, -0.268087, 0.211975)36.960999, 16.5103, 3.24869
9given(0.368054, 0.833552, 0.41198), (0.832352, -0.492846, 0.253561), (0.414399, 0.249588, -0.875202)1.09766, -23.6759, 44.047699
10given(0.605018, -0.023149, -0.795876), (-0.022006, -0.999682, 0.012348), (-0.795908, 0.010043, -0.605334)29.838499, 0.066814, 60.8288
Detailsbiological unit is the same as asymmetric unit.

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Components

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


Mass: 21955.988 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 / Gene: clpP, COXBURSA331_A1213 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: A9NDG0, UniProt: Q83DJ2*PLUS, endopeptidase Clp
#2: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1355 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG400, 10mM calcium chloride, 100mM potassium chloride, 50mM HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2009 / Details: bimorph KB mirrors
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→37.5 Å / Num. all: 115581 / Num. obs: 115464 / % possible obs: 99.9 % / Observed criterion σ(F): 1.85 / Observed criterion σ(I): 3.4 / Redundancy: 6.8 % / Biso Wilson estimate: 33.44 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 17.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3.4 / Num. unique all: 11457 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→37.49 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.3 / σ(F): 1.44 / σ(I): 3.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 5754 5.02 %random
Rwork0.1701 ---
all0.172 114887 --
obs0.172 114715 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.803 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 331.96 Å2 / Biso mean: 39.224 Å2 / Biso min: 14.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.0477 Å2-0 Å2-3.8382 Å2
2---6.3198 Å2-0 Å2
3---6.2721 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20585 0 259 1355 22199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921130
X-RAY DIFFRACTIONf_angle_d1.11928459
X-RAY DIFFRACTIONf_chiral_restr0.0773216
X-RAY DIFFRACTIONf_plane_restr0.0053717
X-RAY DIFFRACTIONf_dihedral_angle_d14.7327985
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11L1494X-RAY DIFFRACTIONPOSITIONAL0.344
12M1494X-RAY DIFFRACTIONPOSITIONAL0.344
21B1406X-RAY DIFFRACTIONPOSITIONAL0.472
22C1406X-RAY DIFFRACTIONPOSITIONAL0.472
23D1398X-RAY DIFFRACTIONPOSITIONAL0.627
24G1398X-RAY DIFFRACTIONPOSITIONAL0.673
25H1406X-RAY DIFFRACTIONPOSITIONAL0.432
26I1406X-RAY DIFFRACTIONPOSITIONAL0.224
31K1430X-RAY DIFFRACTIONPOSITIONAL0.715
32N1430X-RAY DIFFRACTIONPOSITIONAL0.715
41A1429X-RAY DIFFRACTIONPOSITIONAL0.345
42E1429X-RAY DIFFRACTIONPOSITIONAL0.345
43F1429X-RAY DIFFRACTIONPOSITIONAL0.487
44J1429X-RAY DIFFRACTIONPOSITIONAL0.412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.590.27295510.214310836113871138799.8
2.59-2.690.23815750.189710858114331143699.9
2.69-2.820.25415970.1974108641146111462100
2.82-2.960.24315560.1905108871144311442100
2.96-3.150.2275700.1798108791144911452100
3.15-3.390.22266080.1797108741148211482100
3.39-3.730.2155800.17210911114911149299.9
3.73-4.270.17975810.148510925115061150999.9
4.27-5.380.16515700.138110940115101151499.9
5.38-37.490.19475660.173110987115531158899.1

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