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- PDB-5e7p: Crystal Structure of MSMEG_0858 (Uniprot A0QQS4), a AAA ATPase. -

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Basic information

Entry
Database: PDB / ID: 5e7p
TitleCrystal Structure of MSMEG_0858 (Uniprot A0QQS4), a AAA ATPase.
ComponentsCell division control protein Cdc48
KeywordsHYDROLASE / AAA ATPase / M. Smegmatic / RecA
Function / homology
Function and homology information


cell division / ATP hydrolysis activity / ATP binding
Similarity search - Function
Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core ...Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TRIETHYLENE GLYCOL / Cell division control protein Cdc48
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.507 Å
AuthorsUnciulac-Carp, M. / Smith, P. / Shuman, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI64693 United States
CitationJournal: J.Bacteriol. / Year: 2016
Title: Crystal Structure and Biochemical Characterization of a Mycobacterium smegmatis AAA-Type Nucleoside Triphosphatase Phosphohydrolase (Msm0858).
Authors: Unciuleac, M.C. / Smith, P.C. / Shuman, S.
History
DepositionOct 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein Cdc48
B: Cell division control protein Cdc48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,88712
Polymers156,4072
Non-polymers2,48010
Water5,981332
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A: Cell division control protein Cdc48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4366
Polymers78,2031
Non-polymers1,2335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division control protein Cdc48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4506
Polymers78,2031
Non-polymers1,2475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.801, 111.816, 151.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cell division control protein Cdc48 / Conserved ATPase


Mass: 78203.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0858, MSMEI_0839 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QQS4, vesicle-fusing ATPase

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Non-polymers , 5 types, 342 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: purified protein 6.5 mg/ml was mixed with equal volume of 0.3 M ammonium tartrate dibasic and 25% polyethylene glycol 3350.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→29.516 Å / Num. obs: 51244 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 37.8 Å2 / Rsym value: 0.075 / Net I/σ(I): 15.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIXdev_833refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.507→29.516 Å / SU ML: 0.71 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2603 5.08 %Random Selection
Rwork0.2059 ---
obs0.2082 51210 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.699 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso mean: 49.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.9373 Å20 Å2-0 Å2
2--16.1876 Å2-0 Å2
3----11.2503 Å2
Refinement stepCycle: LAST / Resolution: 2.507→29.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10412 0 159 332 10903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310739
X-RAY DIFFRACTIONf_angle_d0.7714684
X-RAY DIFFRACTIONf_dihedral_angle_d13.3923945
X-RAY DIFFRACTIONf_chiral_restr0.0441812
X-RAY DIFFRACTIONf_plane_restr0.0031901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5067-2.55230.34751290.29032530X-RAY DIFFRACTION100
2.5523-2.60130.32011290.28962514X-RAY DIFFRACTION100
2.6013-2.65440.36771290.27342551X-RAY DIFFRACTION100
2.6544-2.71210.3691260.28852527X-RAY DIFFRACTION100
2.7121-2.77510.35751340.26062531X-RAY DIFFRACTION100
2.7751-2.84450.33061420.25182522X-RAY DIFFRACTION100
2.8445-2.92130.27941470.24632506X-RAY DIFFRACTION99
2.9213-3.00720.30651370.24872544X-RAY DIFFRACTION99
3.0072-3.10420.28381500.23522501X-RAY DIFFRACTION99
3.1042-3.2150.26991430.21632537X-RAY DIFFRACTION100
3.215-3.34350.24061300.21322544X-RAY DIFFRACTION100
3.3435-3.49550.27291390.21682544X-RAY DIFFRACTION100
3.4955-3.67940.26341470.19162531X-RAY DIFFRACTION100
3.6794-3.90950.2371430.18172576X-RAY DIFFRACTION100
3.9095-4.21050.20881360.16722561X-RAY DIFFRACTION100
4.2105-4.63280.18671330.152587X-RAY DIFFRACTION100
4.6328-5.29980.21951370.1742608X-RAY DIFFRACTION100
5.2998-6.66450.2451320.2282652X-RAY DIFFRACTION100
6.6645-29.51780.18531400.17152741X-RAY DIFFRACTION99
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)
12.03540.0391-0.88510.49540.03541.6777-0.17760.2391-0.55240.04590.01350.060.55290.1532-0.01220.29910.12950.11460.3044-0.13520.315869.808939.917269.8504
22.5105-0.84320.59491.0507-0.35331.9928-0.05050.2497-0.4115-0.001-0.0220.14890.2362-0.1195-0.02750.1537-0.06730.04920.1662-0.05980.178247.939251.538375.0788
32.2705-0.6178-0.33041.21520.45250.82180.06140.25670.2456-0.1257-0.0687-0.0175-0.11810.2493-0.0090.1447-0.03670.02170.22910.04440.127470.011472.414581.4308
41.8969-0.0072-0.02711.142-0.00451.7378-0.0024-0.1303-0.49910.03580.0184-0.12930.615-0.39310.02160.3359-0.18040.08250.1780.15410.211319.981142.1976119.1348
52.69110.53270.62651.25720.43142.7615-0.08550.0205-0.2414-0.09860.0328-0.17330.24150.2319-0.03430.18960.04570.04350.05260.05880.147640.21153.6029111.3859
62.66690.6035-0.02561.0374-0.37151.6515-0.0683-0.31870.30020.1679-0.0219-0.0578-0.33-0.4466-0.11760.17110.0789-0.02630.0811-0.01540.079817.179972.3477105.4128
70.0272-0.06580.0440.35810.02540.1601-0.0866-0.406-0.66150.71750.01150.24740.7622-0.0724-0.0010.41540.01660.05710.39330.05030.427750.364747.713379.1167
80.3923-0.79250.26462.54480.20660.95530.17090.6010.2976-0.4751-0.09160.1344-0.1773-0.34310.22760.3720.1572-0.12811.050.12820.714275.438767.871778.7528
91.4032-0.5698-0.91890.58010.67530.8634-0.23040.2364-0.8639-0.5859-0.0806-0.31060.70140.1145-0.28470.43860.0435-0.00180.1589-0.02390.370836.802648.8372108.8841
100.05570.3028-0.08161.917-0.66890.30870.2575-0.1430.43310.4016-0.0547-0.0518-0.3370.1820.00220.36810.04420.04131.0306-0.30980.744111.876168.8214108.1598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 17:184)
2X-RAY DIFFRACTION2chain 'A' and (resseq 185:483)
3X-RAY DIFFRACTION3chain 'A' and (resseq 484:744)
4X-RAY DIFFRACTION4chain 'B' and (resseq 18:218)
5X-RAY DIFFRACTION5chain 'B' and (resseq 219:471)
6X-RAY DIFFRACTION6chain 'B' and (resseq 472:744)
7X-RAY DIFFRACTION7chain 'A' and resseq 901
8X-RAY DIFFRACTION8chain 'A' and resseq 902
9X-RAY DIFFRACTION9chain 'B' and resseq 901
10X-RAY DIFFRACTION10chain 'B' and resseq 902

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