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- PDB-3m9h: Crystal structure of the amino terminal coiled coil domain of the... -

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Basic information

Entry
Database: PDB / ID: 3m9h
TitleCrystal structure of the amino terminal coiled coil domain of the Mycobacterium tuberculosis proteasomal ATPase Mpa
ComponentsProteasome-associated ATPase
KeywordsCHAPERONE / four helix antiparallel bundle / ATP-binding / Nucleotide-binding / Proteasome / S-nitrosylation / Virulence
Function / homology
Function and homology information


ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / proteasome-activating nucleotidase complex / symbiont-mediated perturbation of host defenses / response to nitrosative stress / cell wall / proteasomal ubiquitin-independent protein catabolic process / ATP-dependent peptidase activity / protein unfolding / proteasomal protein catabolic process ...ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / proteasome-activating nucleotidase complex / symbiont-mediated perturbation of host defenses / response to nitrosative stress / cell wall / proteasomal ubiquitin-independent protein catabolic process / ATP-dependent peptidase activity / protein unfolding / proteasomal protein catabolic process / cellular response to nitric oxide / peptidoglycan-based cell wall / modification-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / : / ATPase, AAA-type, conserved site / AAA-protein family signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / : / ATPase, AAA-type, conserved site / AAA-protein family signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Proteasome-associated ATPase / Proteasome-associated ATPase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, H. / Wang, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation.
Authors: Wang, T. / Darwin, K.H. / Li, H.
History
DepositionMar 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasome-associated ATPase
B: Proteasome-associated ATPase
C: Proteasome-associated ATPase
D: Proteasome-associated ATPase
E: Proteasome-associated ATPase
F: Proteasome-associated ATPase


Theoretical massNumber of molelcules
Total (without water)37,4886
Polymers37,4886
Non-polymers00
Water1,08160
1
A: Proteasome-associated ATPase
B: Proteasome-associated ATPase
C: Proteasome-associated ATPase
D: Proteasome-associated ATPase


Theoretical massNumber of molelcules
Total (without water)24,9924
Polymers24,9924
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-67 kcal/mol
Surface area9910 Å2
MethodPISA
2
E: Proteasome-associated ATPase

E: Proteasome-associated ATPase

E: Proteasome-associated ATPase

E: Proteasome-associated ATPase


Theoretical massNumber of molelcules
Total (without water)24,9924
Polymers24,9924
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area8500 Å2
ΔGint-64 kcal/mol
Surface area9790 Å2
MethodPISA
3
F: Proteasome-associated ATPase

F: Proteasome-associated ATPase

F: Proteasome-associated ATPase

F: Proteasome-associated ATPase


Theoretical massNumber of molelcules
Total (without water)24,9924
Polymers24,9924
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544x,-y-1/2,-z-1/21
crystal symmetry operation11_554-x+1/2,y,-z-1/21
crystal symmetry operation14_545-x+1/2,-y-1/2,z1
Buried area8520 Å2
ΔGint-63 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.752, 114.164, 114.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11E-102-

HOH

21F-36-

HOH

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Components

#1: Protein
Proteasome-associated ATPase / AAA ATPase forming ring-shaped complexes / ARC / Mycobacterial proteasome ATPase


Mass: 6248.081 Da / Num. of mol.: 6 / Fragment: Coil coil domain (UNP residues: 46-96)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: mpa / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P63345, UniProt: P9WQN5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3

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Sample preparation

CrystalDensity Matthews: 1.76 Å3/Da / Density % sol: 30.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M sodium citrate, 2.1M ammonium sulfate, 0.24M sodium/potassium tartrate 0.25M sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.9795
SYNCHROTRONNSLS X29A20.9193
SYNCHROTRONNSLS X29A31.0809
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJan 30, 2010
ADSC QUANTUM 3152CCDJan 22, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
3Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.91931
31.08091
ReflectionResolution: 2→25 Å / Num. all: 18001 / Num. obs: 17050 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 14.5 % / Rmerge(I) obs: 0.085
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.541 / Num. unique all: 890 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.967 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.274 921 5.1 %RANDOM
Rwork0.206 ---
obs0.209 17050 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 132.73 Å2 / Biso mean: 38.744 Å2 / Biso min: 14.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 0 60 2148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0212088
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9952784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0345252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26623.158114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7915450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4681536
X-RAY DIFFRACTIONr_chiral_restr0.1110.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021512
X-RAY DIFFRACTIONr_mcbond_it2.4341.51284
X-RAY DIFFRACTIONr_mcangle_it4.35722034
X-RAY DIFFRACTIONr_scbond_it5.9933804
X-RAY DIFFRACTIONr_scangle_it10.0474.5750
X-RAY DIFFRACTIONr_rigid_bond_restr3.32532050
LS refinement shellResolution: 2→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 45 -
Rwork0.176 1205 -
all-1250 -
obs--94.84 %
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)
11.0714-0.2253-0.00191.354-2.74589.15610.06410.0503-0.0077-0.0804-0.2519-0.1480.11230.34580.18770.10620.0048-0.01240.1217-0.020.14933.8041-6.2635-22.5628
20.81-0.41160.20849.1399-3.22421.2577-0.1115-0.0469-0.00030.27330.26690.1389-0.1139-0.1972-0.15540.15210.01920.01560.17440.00670.146916.3427-5.7843-22.3998
32.06432.921-3.08244.4199-5.07726.79110.06740.04420.09120.2580.03030.1387-0.3793-0.1141-0.09770.13750.0070.01260.1463-0.02060.14389.9209-12.6748-24.8647
42.0796-3.10642.8926.5509-4.68594.17870.13730.06380.0375-0.4326-0.1308-0.08920.31110.1636-0.00650.13460.0197-0.00180.1583-0.01290.137810.4353-3.9996-15.7597
54.1867-0.81510.05930.2757-0.12920.1223-0.0107-0.13220.03630.03420.02350.0266-0.0214-0.0006-0.01280.136-0.00670.00470.14850.00760.14451.2778-4.5298-4.2288
611.7199-1.3874-2.12370.22360.35850.6239-0.1682-0.2306-0.1796-0.01170.05750.04690.00970.00480.11070.1386-0.0143-0.01420.1215-0.00030.14921.7162-24.3637-33.186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 94
2X-RAY DIFFRACTION2B52 - 94
3X-RAY DIFFRACTION3C52 - 94
4X-RAY DIFFRACTION4D52 - 94
5X-RAY DIFFRACTION5E52 - 94
6X-RAY DIFFRACTION6F52 - 94

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